Reference clones and sequences for non-subtype B isolates of human immunodeficiency virus type 1

ABSTRACT

The nucleotide sequences of the genomes of eleven molecular clones for non-subtype B isolates of human immunodeficiency virus type 1 are disclosed. The invention relates to the nucleic acids and peptides encoded by and/or derived from these sequences and their use in diagnostic methods and as immunogens.

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This is a divisional application of non-provisional U.S. Ser. No. 09/184,418, filed Nov. 2, 1998.

FEDERAL FUNDING LEGEND

[0002] This work was funded by grants RO1 AI25291; and NO1 AI35170 from the National Institutes of Health. Therefore, the government may have certain rights in the invention.

BACKGROUND

[0003] 2. Field of the Invention

[0004] The present invention is in the field of virology. The invention relates to the nucleotide sequences of the genomes of 11 molecular clones for non-subtype B isolates of human immunodeficiency virus type 1 (HIV-1), and nucleic acids derived therefrom. This invention also relates to peptides encoded by and/or derived from the nucleic acid sequences of these molecular clones, and host cells containing these nucleic acid sequences and peptides. The invention also relates to diagnostic methods, kits and immunogens which employ the nucleic acids, peptides and/or host cells of the invention.

[0005] 2. Description of the Related Art

[0006] A critical question facing current AIDS vaccine development efforts is to what extent HIV-1 genetic variation has to be considered in the design of candidate vaccines (11,21,42,72). Phylogenetic analyses of globally circulating viral strains have identified two distinct groups of HIV-1, a major M group and an O group (33,45,61,62). Within the M group, ten sequence subtypes (A-J) have been proposed (29,30,45,72). Sequence variation among viruses belonging to these different lineages is extensive, with envelope amino acid sequence variation ranging from 24% between different subtypes to 47% between the two different groups. Given this extent of diversity, the question has been raised whether immunogens based on a single virus strain can be expected to elicit immune responses effective against a broad spectrum of viruses, or whether vaccine preparations should include mixtures of genetically divergent antigens and/or be tailored toward locally circulating strains (11, 21, 42, 72). This is of particular concern in developing countries where multiple subtypes of HIV-1 are known to co-circulate and where subtype B viruses, which have been the source for most current candidate vaccine preparations (10, 21), are rare or nonexistent (5, 24, 40, 72).

[0007] Although the extent of global HIV-1 variation is well defined, little is known about the biological consequences of this genetic diversity and its impact on cellular and humoral immune responses in the infected host. In particular, it remains unknown whether subtype specific differences in virus biology exist that need to be considered for vaccine design. Only a comprehensive analysis of genetically defined representatives of the various groups and subtypes will address the question of whether certain variants differ in fundamental viral properties and whether such differences will need to be incorporated into vaccine strategies. Obviously, such studies require well-characterized reference reagents, in particular full length and replication competent molecular clones that can be used for functional and biological studies.

[0008] Full-length reference sequences representing the various subtypes are also urgently needed for phylogenetic comparisons. Until about 1994, it was generally thought that individuals do not become infected with multiple distinct HIV-1 strains, and so the possibility that recombination between divergent viruses could contribute to the evolution of HIV-1 was not widely considered. However, recent analyses of subgenomic (23,52,54,58) as well as full-length HIV-1 sequences (7,18,53,60) identified a surprising number of HIV-1 strains which clustered in different subtypes in different parts of their genome. All of these originated from geographic regions where multiple subtypes co-circulated and are the results of co-infections with highly divergent viruses (52,60,62).

[0009] Recombinant viruses can be detected because their phylogenetic affinities vary depending on the region of genome analyzed. A useful initial approach is to examine the extent of sequence divergence/similarity between a new sequence and a bank of reference sequences of different subtypes, for example as a diversity plot (18), or using the RIP program (75); if the extent of relative similarity to different subtypes varies along the sequence, this may indicate that the sequence is a recombinant. However, fuller investigation must involve a phylogenetic approach, comparing trees derived by analyses of different regions of the genome, and assessing the confidence of phylogenetic clustering by a statistical approach such as the bootstrap. A thorough analysis would involve taking a window of sequence of a certain size, and moving this window along the genome in steps of a defined size, generating perhaps hundreds of trees for visual examination in the process. There are at least two short cuts. One is to analyze only a few windows, defining selected regions according to the output of the diversity analysis. Another is to not examine the entire phylogenetic tree of all subtypes, but to focus on one particular phylogenetic question. Thus, if the initial analyses suggest that a sequence may be a recombinant between two particular subtypes, it is possible to ask simply what is the bootstrap value for the clustering of the new sequence with one or another particular subtype, and plot these values as a function of position along the genome; this is the basis of the “bootscanning” approach (57). Once the subtypes putatively involved in the recombination event have been identified, and the crossover points have been approximately localized, more precisely defined breakpoints can be determined, and their statistical significance assessed, using informative site analysis (19, 52, 53).

[0010] Detailed phylogenetic characterization revealed that most of the recombinant viruses have a complex genome structure with multiple points of crossover (7,18,53,60). Some recombinants, like the “subtype E” viruses, which are in fact A/E recombinants (7,18), have a wide-spread geographic dissemination and are responsible for much of the Asian HIV-1 epidemic (69,70). In other areas, recombinants appear to be generated with increasing frequencies as many randomly chosen isolates exhibit evidence of mosaicism (4,8,31,66,71).

[0011] Since recombination provides the opportunity for evolutionary leaps with genetic consequences that are far greater than the steady accumulation of individual mutations, the impact of recombination on viral properties must be monitored. Full-length non-recombinant reference sequences for all major HIV-1 groups and subtypes are thus needed to map and characterize the extent of inter-subtype recombination.

[0012] Non-subtype B viruses cause the vast majority of new HIV-1 infections worldwide. Although their geographic dissemination is carefully monitored, their immunogenic and biological properties remain largely unknown, in part because well-characterized virological reference reagents are lacking. In particular, full length clones and sequences are rare, since subtype classification is frequently based on small PCR-derived viral fragments. There are currently only five full length, non-recombinant molecular clones available for viruses other than subtype B (45), and these represent only three of the proposed (group M) subtypes (A, C and D). Moreover, only three clones (all derived from subtype D viruses) are replication competent and thus useful for studies requiring functional gene products (45,48,65). Given the unknown impact of genetic variation on correlates of immune protection, subtype specific reagents are critically needed for phylogenetic, immunological and biological studies.

SUMMARY OF INVENTION

[0013] The present invention pertains to the isolation and characterization of the genomic sequences of 11 molecular clones for non-subtype B HIV-1 isolates of human immunodeficiency virus type 1 (HIV-1), and nucleic acids derived therefrom. Of these 11 molecular clones, 94IN476.104, 96ZM651.8, and 96ZM751.3 are non-mosaic reference clones of HIV-1 subtype C; 93BR020.1 is a reference clone of HIV-1 subtype F; 90CF056.1 is a reference clone of HIV-1 subtype H; 92RW009.6 is a double recombinant of HIV-1 subtypes A/C; 92NG083.2 and 92NG003.1 are double recombinants of HIV-1 subtypes A/G; 93BR029.4 is a double recombinant of HIV-1 subtypes B/F; 94CY017.41 is a double recombinant of HIV-1 subtype A and a new, as yet undefined, subtype; and 94CY032.3 is a triple recombinant of HIV-1 subtypes A/G/I.

[0014] In particular, the present invention relates to nucleic acids comprising the genomic sequences of one or more of these 11 clones for non-subtype B HIV-1 isolates, as well as nucleic acids comprising the complementary (or antisense) sequence of one or more of the genomic sequences of these 11 clones, and nucleic acids derived therefrom.

[0015] The invention also relates to vectors comprising the nucleic acid genomic sequence of one or more of these 11 clones, as well as nucleic acids comprising the complementary (or antisense) sequence of one or more of the genomic sequences of these clones, and nucleic acids derived therefrom.

[0016] The invention also relates to cultured host cells comprising the nucleic acid genomic sequences of one or more of these 11 clones for non-subtype B HIV-1 isolates, as well as nucleic acids comprising the complementary (or antisense) sequence of one or more of the genomic sequences of these clones, and nucleic acids derived therefrom.

[0017] The invention also relates to host cells containing vectors comprising the genomic sequences of one or more of these 11 clones for non-subtype B HIV-1 isolates, as well as nucleic acids comprising the complementary (or antisense) sequence of one or more of the genomic sequences of these clones, and nucleic acids derived therefrom.

[0018] The invention also relates to synthetic or recombinant polypeptides encoded by or derived from the nucleic acid sequences of one or more of the genomes of these 11 clones for non-subtype B HIV-1 isolates, and fragments thereof.

[0019] The invention also relates to methods for producing the polypeptides of the invention in culture using one or more of these 11 clones for non-subtype B HIV-1 viruses or nucleic acids derived therefrom, including recombinant methods for producing the polypeptides of the invention.

[0020] The invention further relates to methods of using the polypeptides of the invention as immunogens to stimulate an immune response in a mammal, such as the production of antibodies, or the generation of cytotoxic or helper T-lymphocytes.

[0021] The invention also relates to methods of using the polypeptides of the invention to detect antibodies which immunologically react with non-subtype B HIV-1 viruses in a mammal or in a biological sample.

[0022] The invention also relates to kits for the detection of antibodies specific for non-subtype B HIV-1 viruses in a biological sample where said kit contains at least one polypeptide encoded by or derived from the nucleic acid sequences of the invention.

[0023] The invention also relates to antibodies, which immunologically react with the virions of one or more of these 11 viruses and/or their encoded polypeptides.

[0024] The invention also relates to methods of detecting virions of non-subtype B HIV-1 viruses and/or their encoded polypeptides, or fragments thereof, using antibodies of the invention.

[0025] The invention also relates to kits for detecting the virions of non-subtype B HIV-1 viruses and/or their encoded polypeptides, wherein the kit comprises at least one antibody of the invention.

[0026] The invention also relates to a method for detecting the presence of non-subtype B HIV-1 viruses in a mammal or a biological sample, said method comprising analyzing the DNA or RNA of a mammal or a sample for the presence of the RNAs, cDNAs or genomic DNAs which will hybridize to a nucleic acid derived from one or more of these 11 non-subtype B HIV-1 molecular clones. Usually, when a completely complementary probe is used, high stringency conditions are desirable in order to prevent false positives. However, conditions of high stringency should only be used if the probes are complementary to target regions which lack heterogeneity. The stringency of hybridization is determined by a number of factors during hybridization and during the washing procedure, including temperature, ionic strength, length of time, and concentration of formamide, if any. The nucleic acid sequences used in probes should be unique to HIV, i.e., the nucleic acid sequences should be absent from individuals not infected with HIV.

[0027] The invention also provides diagnostic kits for the detection of non-subtype B HIV-1 viruses in a mammal using the nucleic acids of the invention. In one embodiment, the kit comprises nucleic acids having sequences useful as hybridization probes in determining the presence or absence of the RNAs, cDNAs or genomic DNAs of non-subtype B HIV-1 viruses. In another embodiment, the kit comprises nucleic acids having sequences useful as primers for reverse-transcription polymerase chain reaction (RT-PCR) analysis of RNA for the presence of HIV-1 viruses in a biological sample.

[0028] The invention further relates to isolated and substantially purified nucleic acids, polypeptides and/or antibodies of the invention.

[0029] The invention further relates to compositions comprising one or more of the nucleic acids, polypeptides and/or antibodies of the invention.

[0030] The invention also relates to computer-generated alignments of the nucleic acid sequences of the viral genomes clones of the 11 clones of this invention, as well as alignments of the encoded amino acid sequences. These sequence alignments serve to highlight regions of homology and non-homology between different sequences and hence, can be used in preparing diagnostic reagents as described herein.

BRIEF DESCRIPTION OF THE DRAWINGS

[0031] So that the matter in which the above-recited features, advantages and objects of the invention, as well as others that will become clear, are attained and can be understood in detail, more particular descriptions of the invention briefly summarized above may be had by reference to certain embodiments thereof that are illustrated in the appended drawings. These drawings form a part of the specification. It is to be noted, however, that the appended drawings illustrate preferred embodiments of the invention and therefore are not to be considered limiting in their scope.

[0032] FIGS. 1A-1B. Phylogenetic relationships of the 11 viral genomes described in this patent application (highlighted) to representatives of all major HIV-1 (group M) subtypes in gag (FIG. 1A) and env (FIG. 1B) regions. Trees were constructed from full-length gag and env nucleotide sequences using the neighbor joining method (see text for details of methodology). Horizontal branch lengths are drawn to scale; vertical separation is for clarity only. Values at the nodes indicate the percent bootstraps in which the cluster to the right was supported (bootstrap values of 75% and higher are shown). Asterisks denote hybrid genomes as determined by additional analyses. Brackets at the right represent the major sequence subtypes of HIV-1 group M. Trees were rooted by using SIVcpzGAB as an outgroup.

[0033] FIGS. 2A-2J. Diversity plots comparing the sequence relationships of the 11 viral genomes described in this patent application to each other and to reference sequences from the database. In each of FIGS. 2A-2J, the sequence named above the plots is compared to the sequences listed at the right. U455, LAI, C2220, and NDK are published reference sequences for subtypes A, B, C and D, respectively. Distance values were calculated for a window of 500 bp moved in steps of 10 nucleotides. The x-axis indicates the nucleotide positions along the alignment (gaps were stripped and removed from the alignment). The positions of the start codons of the gag, pol, vif, vpr, env, and nef genes are shown. The y-axis denotes the distance between the viruses compared (0.05=5% divergence).

[0034] FIGS. 3A-3I. Exploratory tree analysis. Neighbor joining trees were constructed for a 500 bp window moved in increments of 100 bp along the multiple genome alignment. Trees depicting discordant branching orders among four of the 11 sequences included in this patent application are shown in FIGS. 3A-3I (hybrid sequences are boxed). The position of each tree in the alignment is indicated; subtypes are identified by brackets. Numbers at nodes indicate the percentage of bootstrap values with which the adjacent cluster is supported (only values above 80% are shown). Branch lengths are drawn to scale.

[0035] FIGS. 4A-4B. Recombination breakpoint analysis for 92RW009.6 and 93BR029.4. (FIG. 4A) Bootstrap plots depicting the relationship of 92RW009.6 to representatives of subtype A and C, respectively. Trees were constructed from the multiple genome alignment and the magnitude of the bootstrap value supporting the clustering of 92RW009.6 with U455 and 92UG037.1 (subtype A), or C2220 and 92BR025.8 (subtype C), respectively, was plotted for a window of 500 bp moved in increments of 10 bp along the alignment. Regions of subtype A or C origin are identified by very high bootstrap values (>90%). Points of cross-over of the two curves indicate recombination breakpoints. The beginning of gag, pol, vif, vpr, env and nef open reading frames are shown. The y-axis indicates the percent bootstrap replicates, which support the clustering of 92RW009.6 with representatives of the respective subtypes. (FIG. B) Bootstrap plots depicting the relationship of 93BR029.4 to representatives of subtype Band F, respectively. Analyses are as in FIG. 4A, except that bootstrap values supporting the clustering of 93BR029.4 with SF2, OYI, MN, LAI and RF (subtype B), or 93BR020.1 (subtype F), respectively, were plotted. Subtype D viruses were excluded from this analysis because of their known close relationship with subtype B viruses.

[0036] FIGS. 5A-5D. Recombination breakpoint analysis of 92NG083.2 and 92NG003.1. Neighbor joining trees depicting discordant branching orders of 92NG003.1 and 92NG083.2 in regions delineated by breakpoints identified by distance plots (not shown) are shown in FIGS. 5A-5D (hybrid sequences are boxed). The position of each tree in the alignment is indicated; subtypes are identified by brackets. Numbers at nodes indicate the percentage of bootstrap values with which the adjacent cluster is supported (only values above 80% are shown). Branch lengths are drawn to scale.

[0037]FIG. 6. Inferred structure of the five recombinant genomes included in this patent application. LTR sequences were not analyzed and are thus shown as open boxes.

[0038] FIGS. 7A-7C. Subtype specific genome features. (FIG. 7A) Alignment of deduced Tat (region encoded by second exon) amino acid sequences. Consensus sequences were generated for available representatives of all major subtypes (question marks indicate sites at which fewer than 50% of the viruses contain the same amino acid residue). Dashes denote sequence identity with the consensus sequence, while dots represent gaps introduced to optimize alignments. A vertical box highlights a premature Tat protein truncation (asterisk) which is present in 11 of 15 subtype D, and 4 of 52 subtype B viruses (frequencies are listed in the column on the right). (FIG. 7B) Alignment of deduced Rev (region encoded by the second exon) protein sequences. (FIG. 7C) Alignment of deduced Vpu protein sequences.

[0039]FIG. 8. Generation of replication competent proviral clones from long PCR products. The general construction scheme of a replication competent provirus from two separately amplified genomic regions is depicted.

[0040]FIG. 9. Diversity plots comparing the sequence relationships of 94CY032.3 to reference sequences from the database. 92UG037.1, LAI, C2220, and ELI are reference sequences for subtypes A, B, C and D, respectively. 92NG083.2 is a known G/A recombinant, but contains only a small subtype A fragment between position 4200 and 4800 (there is presently no full length non-mosaic subtype G reference sequence available). Distance values were calculated for a window of 400 bp moved in steps of 10 nucleotides. The x-axis indicates the nucleotide positions along the alignment (gaps were stripped and removed from the alignment). The positions of the start codons of the gag, pol, vif, vpr, env, and nef genes are shown. The y-axis denotes the distance between the viruses compared (0.05=5% difference).

[0041] FIGS. 10A-10K. Exploratory tree analysis. Neighbor joining trees were constructed for a 400 bp window moved in increments of 10 bp along the multiple genome alignment. Trees in FIGS. 10A-10K depict the discordant branching orders for 94CY032.3 (highlighted). The position of each tree in the alignment is indicated; subtypes are identified by brackets. Numbers at nodes indicate the percentage of bootstrap values with which the adjacent cluster is supported (only values above 80% are shown). Branch lengths are drawn to scale.

[0042]FIG. 11. Bootstrap plot analysis to map recombination breakpoints in 94CY032.3. Bootscanning was performed essentially as described, plotting the magnitude of the bootstrap value supporting the clustering of 94CY032.3 with 92UG037.1 (subtype A ) in comparison with that of 94CY032.3 and 92NG083.2 (“subtype G”) for a window of 400 bp moved in increments of 10 bp along the alignment. Regions of subtype A or G origin are identified by very high bootstrap values (>80%). The location of eight recombination crossovers is indicated. Breakpoint analysis between position 4200 and 4800 was not possible due to the recombinant nature of 92NG083.2. The beginning of gag, pol, vif, vpr, env and nef open reading frames are shown. The y-axis indicates the percent bootstrap replicates, which support the clustering of 94CY032.3 with representatives of the respective subtypes.

[0043]FIG. 12. Recombination breakpoint analysis of 94CY032.3 in the vif/vpr region. Neighbor joining trees depicting the position of 94CY032.3 in regions flanking the breakpoints identified by distance plot analysis (not shown). Trees were constructed from the genomic regions indicated. Subtypes are identified by brackets. Four sequences from Mali represent subtype G (these are the only available subtype G reference sequences in this region, since all other “subtype G” viruses contain A fragments). Numbers at nodes indicate the percentage of bootstrap values with which the adjacent cluster is supported (only values above 80% are shown). Branch lengths are drawn to scale.

[0044] FIGS. 13A-13Z. Nucleotide sequence alignment of the 11 near full-length HIV-1 sequences included in this patent application. Sequences were aligned using CLUSTAL W and adjusted manually using the sequence editor MASE. Dots indicate gaps introduced to optimize the alignment. The beginning and end of all open reading frames are indicated by arrows above or below the alignment. The homologies between the sequences of nucleotides in the eleven independent clones are indicated by dashes. Sequences of nucleotides present uniquely in the various clones (as compared to the corresponding sequences of the other ten clones) are indicated by letters, i.e., the sequences themselves.

[0045] FIGS. 14A-14B. Amino acid sequence alignments of the Gag polypeptides encoded by the 11 near full-length HIV-1 sequences included in this patent application. The homologies between the sequences of amino acids in the various polypeptides encoded by the eleven independent clones are indicated by dashes. Sequences of amino acids present uniquely in the various polypeptides (as compared to the corresponding polypeptides of the other ten clones) are indicated by letters, i.e., the sequences themselves.

[0046] FIGS. 15A-15C. Amino acid sequence alignments of the Pol polypeptides encoded by the 11 near full-length HIV-1 sequences included in this patent application. The homologies between the sequences of amino acids in the various polypeptides encoded by the eleven independent clones are indicated by dashes. Sequences of amino acids present uniquely in the various polypeptides (as compared to the corresponding polypeptides of the other ten clones) are indicated by letters, i.e., the sequences themselves.

[0047]FIG. 16. Amino acid sequence alignments of the Vif polypeptides encoded by the 11 near full-length HIV-1 sequences included in this patent application. The homologies between the sequences of amino acids in the various polypeptides encoded by the eleven independent clones are indicated by dashes. Sequences of amino acids present uniquely in the various polypeptides (as compared to the corresponding polypeptides of the other ten clones) are indicated by letters, i.e., the sequences themselves.

[0048]FIG. 17. Amino acid sequence alignments of the Vpr polypeptides encoded by the 11 near full-length HIV-1 sequences included in this patent application. The homologies between the sequences of amino acids in the various polypeptides encoded by the eleven independent clones are indicated by dashes. Sequences of amino acids present uniquely in the various polypeptides (as compared to the corresponding polypeptides of the other ten clones) are indicated by letters, i.e., the sequences themselves.

[0049]FIG. 18. Amino acid sequence alignments of the Tat polypeptides encoded by the 11 near full-length HIV-1 sequences included in this patent application. The homologies between the sequences of amino acids in the various polypeptides encoded by the eleven independent clones are indicated by dashes. Sequences of amino acids present uniquely in the various polypeptides (as compared to the corresponding polypeptides of the other ten clones) are indicated by letters, i.e., the sequences themselves.

[0050]FIG. 19. Amino acid sequence alignments of the Rev polypeptides encoded by the 11 near full-length HIV-1 sequences included in this patent application. The homologies between the sequences of amino acids in the various polypeptides encoded by the eleven independent clones are indicated by dashes. Sequences of amino acids present uniquely in the various polypeptides (as compared to the corresponding polypeptides of the other ten clones) are indicated by letters, i.e., the sequences themselves.

[0051]FIG. 20. Amino acid sequence alignments of the Vpu polypeptides encoded by the 11 near full-length HIV-1 sequences included in this patent application. The homologies between the sequences of amino acids in the various polypeptides encoded by the eleven independent clones are indicated by dashes. Sequences of amino acids present uniquely in the various polypeptides (as compared to the corresponding polypeptides of the other ten clones) are indicated by letters, i.e., the sequences themselves.

[0052] FIGS. 21A-21C. Amino acid sequence alignments of the Env polypeptides encoded by the 11 near full-length HIV-1 sequences included in this patent application. The homologies between the sequences of amino acids in the various polypeptides encoded by the eleven independent clones are indicated by dashes. Sequences of amino acids present uniquely in the various polypeptides (as compared to the corresponding polypeptides of the other ten clones) are indicated by letters, i.e., the sequences themselves.

[0053]FIG. 22. Amino acid sequence alignments of the Nef polypeptides encoded by the 11 near full-length HIV-1 sequences included in this patent application. The homologies between the sequences of amino acids in the various polypeptides encoded by the eleven independent clones are indicated by dashes. Sequences of amino acids present uniquely in the various polypeptides (as compared to the corresponding polypeptides of the other ten clones) are indicated by letters, i.e., the sequences themselves.

DETAILED DESCRIPTION OF THE INVENTION

[0054] The present invention relates to the determination of the nucleic acid sequences of the complete or near complete genomes of 11 non-subtype B HIV-1 viruses isolated from primary isolates collected at major epicenters of the global AIDS pandemic. The nucleotide sequences of these 11 viruses are shown in FIGS. 13A-13Z (SEQ ID NOS: 1 to 11).

[0055] The phrase “derived from” is used throughout the specification and claims with respect to nucleic acids to describe nucleic acid sequences which correspond to a region of the designated nucleotide sequence. Preferably, the sequence of the region from which the nucleic acid is derived is, or is complementary to, a sequence which is unique to the genome of any one of the 11 clones of this invention. However, more preferably, the sequence of the region from which the nucleic acid is derived is, or is complementary to, a sequence which is unique to the viruses in the subtype corresponding to the subtype of any one of the 11 clones of this invention, and whose uniqueness was unknown prior to the disclosure of the clones of this invention. For example, sequences in the Cyprus clone 94CY032.3 which map to the I region are unique wherever they are not identical to known prior art sequences. Whether or not a sequence is unique to the genome of one of the molecular clones or a subtype can be determined by techniques known to those of skill in the art. For example, the sequence can be compared to sequences in databanks, e.g., GenBank, to determine whether it is present in the uninfected host or other organisms. The sequence can also be compared to the known sequences of other viral agents, including other retroviruses. The correspondence or non-correspondence of the derived sequence to other sequences can also be determined by hybridization under the appropriate stringency conditions. Hybridization techniques for determining the complementarity of nucleic acid sequences are well known in the art. In addition, mismatches of duplex polynucleotides formed by hybridization can be determined by known techniques, including for example, digestion with a nuclease such as S1 that specifically digests single-stranded areas in duplex polynucleotides.

[0056] Regions of the viral genome from which nucleic acid sequences may be derived include, but are not limited to, regions encoding specific epitopes as well as non-transcribed and non-translated sequences. Preferably, the epitope is unique to HIV viruses in the subtype corresponding to the subtype of the corresponding region of a polypeptide encoded by any one of the 11 clones of this invention, and whose uniqueness was unknown prior to the disclosure of the clones of this invention The uniqueness of the epitope may be determined by its immunological reactivity with HIV viruses of the subtype and lack of immunological reactivity with other HIV viruses of the other subtypes. Methods for determining immunological reactivity are known in the art, e.g., radioimmunoassay and ELISA and other assays mentioned herein. The uniqueness of an epitope can also be determined by computer searches of known databases, e.g., for the p6lynucleotide sequences which encode the eptiope, and by amino acid sequence comparisons with other known proteins.

[0057] The derived nucleic acid is not necessarily physically derived from the nucleotide sequence shown, but may be generated in any manner, including for example, chemical synthesis or DNA replication or reverse transcription or transcription, which are based on the information provided by the sequence of bases in the region(s) from which the nucleic acid is derived. The derived nucleic acid is comprised of at least 6-12 bases, more preferably at least 15-19 bases, more preferably at least 30 bases. The derived nucleic acid may also be larger, e.g., at least 100 bases in length, depending on the desired use of the nucleic acid. In addition, regions or combinations of regions corresponding to that of the designated sequence may be modified in ways known in the art to be consistent with an intended use. The derived nucleic acid may be a polynucleotide or polynucleotide analog.

[0058] The term “recombinant nucleotide” or “recombinant nucleic acid” as used herein intends a nucleic acid of genomic, cDNA, semisynthetic, or synthetic origin which, by virtue of its origin or manipulation: (1) is not associated with all or a portion of the nucleic acid with which it is associated in nature; and/or (2) is linked to a nucleic acid other than that to which it is linked in nature.

[0059] The term “polynucleotide” as used herein refers to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. This term refers only to the primary structure of the molecule. Thus, this term includes double- and single-stranded DNA, as well as double- and single-stranded RNA. It also includes modified, for example, by methylation and/or by capping, and unmodified forms of the polynucleotide.

[0060] The present invention relates to nucleic acids having the genomic sequence of any one of the 11 molecular clones for non-subtype HIV-1 isolates of this invention as shown in FIG. 13 (SEQ ID NOS: 1 to 11), as well as fragments (or partial sequences) thereof. The invention also relates to nucleic acids having complementary (or antisense) sequences to the sequences shown in FIGS. 13A-13Z (SEQ ID NOS: 1 to 11), as well as fragments (or partial sequences) thereof. Partial sequences may be obtained by various methods, including restriction digestion of nucleic acids with sequences shown in FIGS. 13A-13Z (SEQ ID NOS: 1 to 11), PCR amplification, and direct synthesis. Partial sequences may be all or part of the LTR and/or other untranslated regions of the genomes of one or more of the 11 viral clones of this invention, and/or all or part of the genes encoding the Gag, Pol, Vif, Vpr, Env, Tat, Rev, Nef and Vpu proteins and/or complementary (or antisense) sequences thereof. Nucleic acids of the invention also include cDNA, mRNA, and other nucleic acids derived from the genomic sequences of one or more of these 11 HIV-1 clones. Sequences of the genes encoding Gag, Pol, Vif, Vpr, Env, Tat, Rev, Nef and Vpu are identified in FIGS. 13A-13Z.

[0061] Genomic sequences of seven of the 11 clones of the invention have been made publicly available. The GenBank Accession numbers are as follows: Sequence Clone Accession No. ID No. 92R W009.6 U88823 4 92NG003.1 U88825 5 92NG083.2 U88826 2 93BR020.1 AF005494 1 93BR029.4 AF005495 6 90CF056.1 AF005496 3 94CY032.3 AF049337 7 94CY017.41 — 10 96ZM651.8 — 8 96ZM751.3 — 9 94IN476.104 — 11

[0062] The nucleic acids of the invention may be present in vectors or host cells in tissue culture or other media. The nucleic acids of the invention may also be isolated and substantially purified by methods known in the art.

[0063] Nucleic acids of about 17 bases to about 35 bases in length are particularly preferred for use as primers in PCR amplification (see, e.g., the primers UP1A and R/U5 (17 mer and 22 mer, respectively) and UP1AMlu1 and Low1Mlu1 (28 mer and 35 mer respectively)). Nucleic acids of about 14 to about 25 bases in length are particularly preferred for use in nucleotide arrays. (See, eg., ref. 108, which uses 20 to 25 mers).

[0064] The present invention also relates to vectors and host cells comprising the nucleic acids of the invention.

[0065] The present invention also relates to compositions comprising one or more of the nucleic acids, vectors, and/or host cells of the invention.

[0066] The present invention further relates to methods of using the nucleic acids, vectors, and/or host cells of the invention, and/or compositions thereof. For example, the invention relates to the use of nucleic acids of the invention as diagnostic agents to detect the presence or absence of non-subtype B HIV-1 viruses in a sample.

[0067] The present invention also relates to a method for detecting the presence of HIV-1 viruses which are related to the viruses of this invention in a mammal, using the nucleic acids of this invention.

[0068] In one embodiment, the detection method involves analyzing DNA obtained from a mammal suspected of harboring HIV-1 viruses. DNA can be isolated by methods well known in the art.

[0069] The methods for analyzing the DNA for the presence of the viruses of this invention include Southern blotting (86), dot and slot hybridization (87), and nucleotide arrays (see, e.g., U.S. Pat. No. 5,445,934 and U.S. Pat. No. 5,733,729).

[0070] The nucleic acid probes used in the detection methods set forth above are derived from nucleic acid sequences shown in FIGS. 13A-13Z (SEQ ID NOS: 1 to 11). The size of such probes is at least 10-12 bases long, more usually at least about 19 bases long, more usually from about 200 to about 500 bases, and often exceeding about 1000 bases.

[0071] The nucleic acid probes of this invention may be DNA or RNA. Nucleic acids can be synthesized using any of the known methods of nucleotide synthesis (see, e.g., refs. 88, 89, 90), or they can be isolated fragments of naturally occurring or cloned DNA. In addition, those skilled in the art would be aware that nucleotides can be synthesized by automated instruments sold by a variety of manufacturers or can be commercially custom ordered and prepared. The probes of this invention may also be nucleotide analogs, such as nucleotides linked by phosphodiester, phosphorothiodiester, methylphosphonodiester, or methylphosphonothiodiester moieties (91) and peptide nucleic acids (PNAs), in which the sugar-phosphate backbone of the polynucleotide is replaced with a polyamide or “pseudopeptide” backbone (92).

[0072] The nucleic acid probes can be labeled using methods known to one skilled in the art. Such labeling techniques can include radioactive labels, biotin, avidin, enzymes and fluorescent molecules (93).

[0073] The nucleic acid probes used in the detection methods set forth above are derived from sequences substantially homologous to one or more of the sequences shown in FIGS. 13A-13Z (SEQ ID NOS: 1 to 11), or their complementary sequences. By “substantially homologous”, as used throughout the specification and claims to describe the nucleic acid sequence of the present invention, is meant a high level of homology between the nucleic acid sequence and one or more of the sequences of FIGS. 13A-13Z (SEQ ID NOS: 1 to 11), or its complementary sequence. Preferably, the level of homology is in excess of 80%, more preferably in excess of 90%, with a preferred nucleic acid sequence being in excess of 95% homologous with a portion of one or more of the sequences shown in FIGS. 13A-13Z (SEQ ID NOS: 1 to 11), or its complement. The size of such probes is usually at least 20 nucleotides, more usually from about 200 to 500 nucleotides, and often exceeding 1000 nucleotides.

[0074] Although complete complementarity is not necessary, it is preferred that the probes are made completely complementary to the corresponding portion of the genome, mRNA or cDNA target of at least one of the 11 viruses of this invention.

[0075] The probes can be packaged into diagnostic kits. Diagnostic kits may include ingredients for labeling and other reagents and materials needed for the particular hybridization protocol in addition to the probes.

[0076] In another embodiment of the invention, the detection method comprises analyzing the RNA of a mammal for the presence of HIV-1 viruses which are related to one or more of the 11 the viruses of this invention. RNA can be isolated by methods well known in the art.

[0077] The methods for analyzing the RNA for the presence of the viruses of this invention include Northern blotting (94), dot and slot hybridization, filter hybridization (95), RNase protection (93), and reverse-transcription polymerase chain reaction (RT-PCR) (96). A preferred method is RT-PCR. In this method, the RNA can be reverse transcribed to first strand cDNA using a nucleic acid primer or primers derived from one or more of the nucleotide sequences shown in FIGS. 13A-13Z (SEQ ID NOS: 1 to 11). Once the cDNAs are synthesized, PCR amplification is carried out using pairs of primers designed to hybridize with sequences in the genomes of one or more of the non-subtype B HIV- 1 viruses of this invention which are an appropriate distance apart (at least about 50 bases) to permit amplification of the cDNA and subsequent detection of the amplification product. Each primer of a pair is a single-stranded nucleic acid of about 20 to about 60 bases in length where one primer (the “upstream” primer) is complementary to the original RNA and the second primer (the “downstream” primer) is complementary to the first strand of cDNA generated by reverse transcriptions of the RNA. The target sequence is generally about 100 to about 300 bases in length but can be as large as 500-1500 bases or more, e.g., 9,000 bases. Optimization of the amplification reaction to obtain sufficiently specific hybridization to the nucleotide sequences of these viruses is well within the skill in the art and is preferably achieved by adjusting the annealing temperature.

[0078] The amplification products of PCR can be detected either directly or indirectly. In one embodiment, direct detection of the amplification products is carried out via labeling of primer pairs. Labels suitable for labeling the primers of the present invention are known to one skilled in the art and include radioactive labels, biotin, avidin, enzymes and fluorescent molecules. The desired labels can be incorporated into the primers prior to performing the amplification reaction. Alternatively, the desired labels can be incorporated into the primer extension products during the amplification reaction in the form of one or more labeled dNTPs. In one embodiment of the present invention, the labeled amplified PCR products can be detected by agarose gel electrophoresis followed by ethidium bromide staining and visualization under ultraviolet light or via direct sequencing of the PCR-products. The labeled amplified PCR products can also be detected by binding to immobilized oligonucleotide arrays.

[0079] In yet another embodiment, unlabelled amplification products can be detected via hybridization with labeled nucleic acid probes in methods known to one skilled in the art, such as dot or slot blot hybridization or filter hybridization.

[0080] The invention also relates to methods of using these nucleic acids to produce polypeptides in vitro or in vivo.

[0081] In one embodiment of the invention, a recombinant method of making a polypeptide of the invention comprises:

[0082] (a) preparing a nucleic acid capable of directing a host cell to produce a polypeptide encoded by the genome of any one of the non-subtype B HIV-1 viruses of this invention;

[0083] (b) cloning the nucleic acid into a vector capable of being transferred into and replicated in a host cell, such vector containing operational elements for expressing the nucleic acid, if necessary;

[0084] (c) transferring the vector containing the nucleic acid and operational elements into a host cell capable of expressing the polypeptide;

[0085] (d) growing the host under conditions appropriate for expression of the polypeptide; and

[0086] (e) harvesting the polypeptide.

[0087] The present invention also relates to non-recombinant methods of making the polypeptides and nucleic acids of the invention. In addition to synthetic methods, the non-recombinant methods involve culturing the viruses of this invention in cell lines, preferably in uninfected human peripheral blood mononuclear cells, under conditions appropriate for expression of the polypeptides and nucleic acids. This invention thus also relates to the polypeptides and nucleic acids produced by the virus in cell culture. The polypeptides and nucleic acids may be isolated and purified by methods known in the art.

[0088] The vectors contemplated for use in the present invention include any vectors into which a nucleic acid sequence as described above can be inserted, along with any preferred or required operational elements, and which vector can then be subsequently transferred into a host cell and, preferably, replicated in such cell. Preferred vectors are those whose restriction sites have been well documented and which contain the operational elements preferred or required for transcription of the nucleic acid sequence. Vectors may also be used to prepare large amounts of nucleic acids of the invention, which may be used, e.g., to prepare probes or other nucleic acid constructs.

[0089] When expression of a polypeptide is desired, the “operational elements” as discussed herein include at least one promoter sequence capable of initiating transcription of the nucleic acid sequence, at least one leader sequence, at least one terminator codon and/or termination signal, and any other DNA sequences necessary or preferred for appropriate transcription and subsequent translation of the vector nucleic acid. In particular, it is contemplated that such vectors will preferably contain at least one origin of replication recognized by the host cell along with at least one selectable marker.

[0090] Preferred expression vectors of this invention are those which function in bacterial and/or eukaryotic cells. Examples of vectors which function in eukaryotic cells include, but are not limited to Venezuelan equine encephalitis virus vectors, simian virus vectors, vaccinia virus vectors, adenovirus vectors, herpes virus vectors, or vectors based on retroviruses, such as murine leukemia virus, or HIV or other lentivirus (97).

[0091] The selected expression vector may be transfected into a suitable bacterial or eukaryotic cell system for purposes of expressing the recombinant polypeptide. Eukaryotic cell systems include but are not limited to cell lines such as HeLa, COS-1, 293T , MRC-5, or CV-1 cells. Primary human cells, such as lymph node cells, macrophages, etc., are also useful in practicing the invention.

[0092] The expressed polypeptides may be detected directly by methods known in the art including, but not limited to, Coomassie blue staining and Western blotting or indirectly, such as in detection of the expression product of a reporter gene, such as luciferase.

[0093] In another embodiment of the invention, the method comprises administering a composition comprising a vector comprising a nucleic acid of the invention to a mammal to produce a polypeptide in vivo.

[0094] The present invention also relates to polypeptides encoded by and/or derived from the nucleotide sequences of this invention. These polypeptides may be natural, synthetic or produced by recombinant methods. Polypeptides can be obtained as a crude lysate or can be purified by standard protein purification procedures known in the art which may include differential precipitation, molecular size exclusion chromatography, ion-exchange chromatography, isolectric focusing, gel electrophoresis and affinity and immunoaffinity chromatography. The polypeptides may be purified by passage through a column containing a resin which has bound thereto antibodies specific for an open reading frame (ORF) polypeptide. The present invention also relates to compositions comprising one or more of the polypeptides of the invention.

[0095] A polypeptide or amino acid sequence derived from a designated nucleic acid sequence refers to a polypeptide having an amino acid sequence identical to that of a polypeptide encoded by the sequence, or a portion thereof wherein the portion consists of at least 6-8 amino acids, and more preferably at least 10 amino acids, and more preferably at least 11-15 amino acids, and most preferably at least 30 amino acids or which is immunologically cross-reactive with a polypeptide encoded by the sequence. The polypeptide may also be larger, e.g., at least 100 amino acids in length, depending on the desired use of the polypeptide. Polypeptides from the V3-loop region and the “crown” of gp4l of Env are particularly preferred.

[0096] A recombinant or derived polypeptide is not necessarily translated from a designated nucleic acid sequence; it may be generated in any manner, including for example, chemical synthesis, or expression of a recombinant expression system, or isolation from any of the 11 HIV-1 viruses of this invention.

[0097] It should be noted that the nucleotide sequences described herein represent one embodiment of the present invention. Due to the degeneracy of the genetic code, it is to be understood that numerous choices of nucleotides may be made that will lead to a sequence capable of directing production of the polypeptides set forth above. As such, nucleic acid sequences which are functionally equivalent to the sequences described herein are intended to be encompassed within the present invention. For example, preferred codons which are appropriate to the host cell may be used (see, e.g., WO 98/34640), or the sequence may be modified to reduce the effect of any inhibitory/instability sequences and to provide for Rev-independent gene expression. (98).

[0098] The polypeptides of this invention consist of at least 6-12 amino acids, more preferably at least 13-18 amino acids, even more preferably at least 19-24 amino acids and most preferably at least 25-30 amino acids encoded by, or otherwise derived from, any one of the genomic sequences shown in FIGS. 13A-13Z (SEQ ID NOS: 1 to 11).

[0099] The present invention further relates to the use of polypeptides of the invention as diagnostic agents.

[0100] In one embodiment, the polypeptides of the invention can be used in immunoassays for detecting the presence of antibodies against non-subtype B HIV-1 viruses in a mammal and for diagnosing the presence of infection of any of these viruses in a mammal.

[0101] For the purposes of the present invention, “mammal” as used throughout the specification and claims, includes, but is not limited to humans, chimpanzees, mangabeys, other primates.

[0102] In a preferred embodiment, test serum is reacted with a solid phase reagent having a surface-bound polypeptide of this invention as an antigen. The solid surface reagent can be prepared by known techniques for attaching polypeptides to solid support material. These attachment methods include non-specific adsorption of the polypeptide to the support or covalent attachment of the polypeptide to a reactive group on the support. After reaction of the antigen with an antibody against any one of the viruses of this invention in the serum, unbound serum components are removed by washing and the antigen-antibody complex is reacted with a secondary antibody such as labeled anti-human antibody. The label may be an enzyme that is detected by incubating the solid support in the presence of a suitable fluorimetric or calorimetric reagent. Other detectable labels may also be used, such as radiolabels or colloidal gold, and the like.

[0103] Immunoassays of the present invention may be a radioimmunoassay, Western blot assay, immunofluorescent assay, enzyme immunoassay, chemiluminescent assay, immunohistochemical assay and the like. Standard techniques for ELISA are well known in the art. Such assays may be a direct, indirect, competitive, or noncompetitive immunoassay as described in the art (see, e.g., ref. 99). Biological samples appropriate for such detection assays include, but are not limited to serum, liver, saliva, lymphocytes or other mononuclear cells.

[0104] Polypeptides of the invention may be prepared in the form of a kit, alone, or in combinations with other reagents such as secondary antibodies, for use in immunoassays.

[0105] In yet another embodiment, the polypeptides of the invention can be used as immunogens to raise antibodies and/or stimulate cellular immunity in a mammal.

[0106] The immunogen may be a partially or substantially purified peptide. Alternatively, the immunogen may be a cell, cell lysate from cells transfected with a recombinant expression vector, or a culture supernatant containing the expressed polypeptide. The immunogen may comprise one or more structural proteins, and/or one or more non-structural proteins of the HIV-1 clones of this invention, or a mixture thereof.

[0107] The effective amount of polypeptide per unit dose sufficient to induce an immune response depends, among other things, on the species of mammal inoculated, the body weight of the mammal and the chosen inoculation regimen, as well as the presence or absence of an adjuvant, as is well known in the art. Inocula typically contain polypeptide concentrations of about 1 microgram to about 50 milligrams per inoculation (dose), preferably about 10 micrograms to about 10 milligrams per dose, most preferably about 100 micrograms to about 5 milligrams per dose.

[0108] The term “unit dose” as it pertains to the inocula refers to physically discrete units suitable as unitary dosages for mammals, each unit containing a predetermined quantity of active material (polypeptide) calculated to produce the desired immunogenic effect in association with the required diluent.

[0109] Inocula are typically prepared as a solution in a physiologically acceptable carrier such as saline, phosphate-buffered saline and the like to form an aqueous pharmaceutical composition.

[0110] The route of inoculation of the polypeptides of the invention is typically parenteral and is preferably intramuscular, sub-cutaneous and the like. The dose is administered at least once. In order to increase the antibody level, at least one booster dose may be administered after the initial injection, preferably at about 4 to 6 weeks after the first dose. Subsequent doses may be administered as indicated.

[0111] To monitor the antibody response of individuals administered the compositions of the invention, antibody titers may be determined. In most instances it will be sufficient to assess the antibody titer in serum or plasma obtained from such an individual. Decisions as to whether to administer booster ihoculations or to change the amount of the composition administered to the individual may be at least partially based on the titer.

[0112] The titer may be based on an immunobinding assay that measures the concentration of antibodies in the serum which bind to a specific antigen. The ability to neutralize in vitro and in vivo biological effects of the viruses of this invention may also be assessed to determine the effectiveness of the immunization.

[0113] For all therapeutic, prophylactic and diagnostic uses, the polypeptide of the invention, alone or linked to a carrier, as well as antibodies and other necessary reagents and appropriate devices and accessories may be provided in kit form so as to be readily available and easily used.

[0114] Where immunoassays are involved, such kits may contain a solid support, such as a membrane (e.g., nitrocellulose), a bead, sphere, test tube, microtiter well, rod, and so forth, to which a receptor such as an antibody specific for the target molecule will bind. Such kits can also include a second receptor, such as a labeled antibody. Such kits can be used for sandwich assays. Kits for competitive assays are also envisioned.

[0115] The immunogens of this invention can also be generated by the direct administration of nucleic acids of this invention to a subject. DNA-based vaccination has been shown to stimulate humoral and cellular responses to HIV-1 antigens in mice (100-103) and macaques (103, 104). More recent studies in infected chimpanzees have shown a possible application of this strategy in HIV-1-infected humans: DNA vaccination of HIV-1-infected chimpanzees with a construct that drives expression of HIV-1 env and rev appeared well-tolerated, and immunized animals demonstrated a boost in antibody response followed by a >1 log decrease in their virus loads (104). A DNA-based vaccine containing HIV-1 env and rev genes was injected into HIV-infected human patients in three doses (30, 100 or 300 micrograms) at 10-week intervals. Increased antibodies against gp120 were observed in the 100 and 300 _g groups. Increases were also noted in cytotoxic T lymphocyte (CTL) activity against gp160-bearing targets and in lymphocyte proliferative activity (105, 106). DNA-based vaccines containing HIV gag genes, with modification of the viral nucleotide sequence to incorporate host-preferred codons (see, e.g., WO 98/34640), and/or to reduce the effect of inhibitory/instability sequences (see, e.g., ref. 98), have likewise been described.

[0116] Therefore, it is anticipated that the direct injection of RNA or DNA vectors of this invention encoding viral antigen can be used for endogenous expression of the antigen to generate the viral antigen for presentation to the immune system without the need for self-replicating agents or adjuvants, resulting in the generation of antigen-specific CTLs and protection from a subsequent challenge with a homologous or heterologous strain of virus.

[0117] CTLs in both mice and humans are capable of recognizing epitopes derived from conserved internal viral proteins and are thought to be important in the immune response against viruses. By recognition of epitopes from conserved viral proteins, CTLs may provide cross-strain protection. CTLs specific for conserved viral antigens can respond to different strains of virus, in contrast to antibodies, which are generally strain-specific.

[0118] Thus, direct injection of RNA or DNA encoding the viral antigen has the advantage of being without some of the limitations of direct peptide delivery or viral vectors (see, e.g., ref. 107 and the discussions and references therein). Furthermore, the generation of high-titer antibodies to expressed proteins after injection of DNA indicates that this may be a facile and effective means of making antibody-based vaccines targeted towards conserved or non-conserved antigens, either separately or in combination with CTL vaccines targeted towards conserved antigens. These may also be used with traditional peptide vaccines, for the generation of combination vaccines. Furthermore, because protein expression is maintained after DNA injection, the persistence of B and T cell memory may be enhanced, thereby engendering long-lived humoral and cell-mediated immunity.

[0119] Nucleic acids encoding a polypeptide of this invention can be introduced into animals or humans in a physiologically or pharmaceutically acceptable carrier using one of several techniques such as injection of DNA directly into human tissues; electroporation or transfection of the DNA into primary human cells in culture (ex vivo), selection of cells for desired properties and reintroduction of such cells into the body, (said selection can be for the successful homologous recombination of the incoming DNA to an appropriate preselected genomic region); generation of infectious particles containing the gag and/or other genes encoded by the viruses of this invention, infection of cells ex vivo and reintroduction of such cells into the body; or direct infection by said particles in vivo. Substantial levels of polypeptide will be produced leading to an efficient stimulation of the immune system.

[0120] Also envisioned are therapies based upon vectors, such as viral vectors containing nucleic acid sequences coding for the polypeptides described herein. These molecules, developed so that they do not provoke a pathological effect, will stimulate the immune system to respond to the polypeptides.

[0121] The effective amount of nucleic acid immunogen per unit dose to induce an immune response depends, among other things, on the species of mammal inoculated, the body weight of the mammal and the chosen inoculation regimen, as is well known in the art. Inocula typically contain nucleic acid concentrations of about 1 microgram to about 50 milligrams per inoculation (dose), preferably about 10 micrograms to about 10 milligrams per dose, most preferably about 100 micrograms to about 5 milligrams per dose.

[0122] Immunization can be conducted by conventional methods. For example, the immunogen can be used in a suitable diluent such as saline or water, or complete or incomplete adjuvants. Further, the immunogen may or may not be bound to a carrier. While it is possible for the immunogen to be administered in a pure or substantially pure form, it is preferable to present it as a pharmaceutical composition, formulation or preparation.

[0123] The formulations of the present invention, both for veterinary and for human use, comprise an immunogen as described above, together with one or more physiologically or pharmaceutically acceptable carriers and optionally other therapeutic ingredients. The carrier(s) must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and not deleterious to the recipient thereof. The formulations may conveniently be presented in unit dosage form and may be prepared by any method well-known in the pharmaceutical art. The immunogen can be administered by any route appropriate for antibody production such as intravenous, intraperitoneal, intramuscular, subcutaneous, and the like. The immunogen may be administered once or at periodic intervals until a significant titer of antibody against any of the 11 viruses of this invention is produced. The antibody may be detected in the serum using an immunoassay. The host serum or plasma may be collected following an appropriate time interval to provide a composition comprising antibodies reactive with the virus particle or encoded polypeptide. The gamma globulin fraction or the IgG antibodies can be obtained, for example, by use of saturated ammonium sulfate or DEAE Sephadex, or other techniques known to those skilled in the art.

[0124] In addition to its use to raise antibodies, the administration of the immunogens of the present invention may be for use as a vaccine for either a prophylactic or therapeutic purpose. When provided prophylactically, a vaccine(s) of the invention is provided in advance of any exposure to any one or more of the 11 non-subtype B viruses of this invention or in advance of any symptoms due to infection of these viruses. The prophylactic administration of a vaccine(s) of the invention serves to prevent or attenuate any subsequent infection of these viruses in a mammal. When provided therapeutically, a vaccine(s) of the invention is provided at (or shortly after) the onset of infection or at the onset of any symptom of infection or any disease or deleterious effects caused by these viruses. The therapeutic administration of the vaccine(s) serves to attenuate the infection or disease. The vaccine(s) of the present invention may, thus, be provided either prior to the anticipated exposure to the viruses of this invention or after the initiation of infection.

[0125] In another embodiment, the polypeptides of the invention can be used to prepare antibodies against epitopes of the viruses of this invention that are useful in diagnosis.

[0126] The term “antibodies” is used herein to refer to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules. Exemplary antibody molecules are intact immunoglobulin molecules, substantially intact immunoglobulin molecules and portions of an immunoglobulin molecule, including those portions known in the art as Fab, Fab′, F(ab′)₂ and F(v) as well as chimeric antibody molecules.

[0127] An antibody of the present invention is typically produced by immunizing a mammal with an immunogen or vaccine of the invention. In one embodiment, the immunogen or vaccine contains one or more polypeptides of the invention, or a structurally and/or antigenically related molecule, to induce, in the mammal, antibody molecules having immunospecificity for the immunizing peptide or peptides. The peptide(s) or related molecule(s) may be monomeric, polymeric, conjugated to a carrier, and/or administered in the presence of an adjuvant. In another embodiment, the immunogen or vaccine contains one or more nucleic acids encoding one or more polypeptides of the invention, or one or more nucleic acids encoding structurally and/or antigenically related molecules, to induce, in the mammal, the production of the immunizing peptide or peptides. The antibody molecules may then be collected from the mammal if they are to be used in immunoassays or for providing passive immunity.

[0128] The antibody molecules of the present invention may be polyclonal or monoclonal. Monoclonal antibodies may be produced by methods known in the art. Portions of immunoglobulin molecules may also be produced by methods known in the art.

[0129] The antibody of the present invention may be contained in various carriers or media, including blood, plasma, serum (e.g., fractionated or unfractionated serum), hybridoma supernatants and the like. Alternatively, the antibody of the present invention is isolated to the extent desired by well known techniques such as, for example, by using DEAE SEPHADEX, or affinity chromatography. The antibodies may be purified so as to obtain specific classes or subclasses of antibody such as IgM, IgG, IgA, IgG₁, IgG₂, IgG₃, IgG4 and the like. Antibody of the IgG class are preferred for purposes of passive protection.

[0130] The presence of the antibodies of the present invention, either polyclonal or monoclonal, can be determined by, but are not limited to, the various immunoassays described above.

[0131] The antibodies of the present invention have a number of diagnostic and therapeutic uses. The antibodies can be used as an in vitro diagnostic agent to test for the presence of any one or more of the 11 HIV-1 viruses of this invention in biological samples in standard immunoassay protocols. Preferably, the assays which use the antibodies to detect the presence of these viruses in a sample involve contacting the sample with at least one of the antibodies under conditions which will allow the formation of an immunological complex between the antibody and the viral antigen that may be present in the sample. The formation of an immunological complex if any, indicating the presence of one or more of these viruses in the sample, is then detected and measured by suitable means. Such assays include, but are not limited to, radioimmunoassays, (RIA), ELISA, indirect immunofluorescence assay, Western blot and the like. The antibodies may be labeled or unlabeled depending on the type of assay used. Labels which may be coupled to the antibodies include those known in the art and include, but are not limited to, enzymes, radionucleotides, fluorogenic and chromogenic substrates, cofactors, biotin/avidin, colloidal gold and magnetic particles. Modification of the antibodies allows for coupling by any known means to carrier proteins or peptides or to known supports, for example, polystyrene or polyvinyl microtiter plates, glass tubes or glass beads and chromatographic supports, such as paper, cellulose and cellulose derivatives, and silica.

[0132] Such assays may be, for example, of direct format (where the labeled first antibody reacts with the antigen), an indirect format (where a labeled second antibody reacts with the first antibody), a competitive format (such as the addition of a labeled antigen), or a sandwich format (where both labeled and unlabelled antibody are utilized), as well as other formats described in the art. In one such assay, the biological sample is contacted with antibodies of the present invention and a labeled second antibody is used to detect the presence of any one of the HIV-1 viruses of this invention, to which the antibodies are bound.

[0133] The antibodies of the present invention are also useful as a means of enhancing the immune response.

[0134] The antibodies may be administered with a physiologically or pharmaceutically acceptable carrier or vehicle therefor. A physiologically acceptable carrier is one that does not cause an adverse physical reaction upon administration and one in which the antibodies are sufficiently soluble and retain their activity to deliver a therapeutically effective amount of the compound. The therapeutically effective amount and method of administration of the antibodies may vary based on the individual patient, the indication being treated and other criteria evident to one of ordinary skill in the art. A therapeutically effective amount of the antibodies is one sufficient to reduce the level of infection by one or more of the viruses of this invention or attenuate any dysfunction caused by viral infection without causing significant side effects such as non-specific T cell lysis or organ damage.

[0135] The route(s) of administration useful in a particular application are apparent to one or ordinary skill in the art. Routes of administration of the antibodies include, but are not limited to, parenteral, and direct injection into an affected site. Parenteral routes of administration include but are not limited to intravenous, intramuscular, intraperitoneal and subcutaneous.

[0136] The present invention includes compositions of the antibodies described above, suitable for parenteral administration including, but not limited to, pharmaceutically acceptable sterile isotonic solutions. Such solutions include, but are not limited to, saline and phosphate buffered saline for intravenous, intramuscular, intraperitoneal, or subcutaneous injection, or direct injection into a joint or other area.

[0137] Antibodies for use to elicit passive immunity in humans are preferably obtained from other humans previously inoculated with pharmaceutical compositions comprising one or more of the polypeptides of the invention. Alternatively, antibodies derived from other species may also be used. Such antibodies used in therapeutics suffer from several drawbacks such as a limited half-life and propensity to elicit an immune response. Several methods are available to overcome these drawbacks. Antibodies made by these methods are encompassed by the present invention and are included herein. One such method is the “humanizing” of non-human antibodies by cloning the gene segment encoding the antigen binding region of the antibody to the human gene segments encoding the remainder of the antibody. Only the binding region of the antibody is thus recognized as foreign and is much less likely to cause an immune response.

[0138] In providing the antibodies of the present invention to a recipient mammal, preferably a human, the dosage of administered antibodies will vary depending upon such factors as the mammal's age, weight, height, sex, general medical condition, previous medical history and the like.

[0139] In general, it is desirable to provide the recipient with a dosage of antibodies which is in the range of from about 5 mg/kg to about 20 mg/kg body weight of the mammal, although a lower or higher dose may be administered. In general, the antibodies will be administered intravenously (IV) or intramuscularly (IM).

[0140] The invention also relates to the use of antisense nucleic acids to inhibit translation of peptides encoded by the HIV-1 viruses of this invention. The antisense nucleic acids are complementary to the viral mRNAs encoding peptides of this invention. The antisense nucleic acids may be in the form of synthetic nucleic acids or they may be encoded by a nucleotide construct, or they may be semi-synthetic. The antisense nucleic acids may be delivered to the cells using methods known to those skilled in the art.

[0141] Kits designed for diagnosis of the HIV-1 viruses of this invention in a biological sample can be constructed by packaging the appropriate materials, including the nucleic acids and/or polypeptides of this invention and/or antibodies which specifically react with antigens of one or more of these viruses, along with other reagents and materials required for the particular assay.

[0142] The present invention further relates to computer-generated alignments of any one or more of the nucleotide sequences shown in FIGS. 13A-13Z (SEQ ID NOS: 1 to 1 1). Computer analysis of the nucleotide sequences, such as the one shown in FIG. 13, can be carried out using commercially available computer program known to one skill in the art.

[0143] In one embodiment, the sequences shown in FIGS. 13A-13Z (SEQ ID NOS: 1 to 11) are aligned by the computer program CLUSTAL (67) and adjusted with multiple-aligned sequence editor (12). The computer analysis results in the distribution of 11 sequences into various genotypes. Five of these sequences represent non-recombinant members of HIV-1 subtypes, and the other six sequences represent HIV-1 intersubtype recombinants.

[0144] The grouping of the molecular clones into mosaic and non-mosaic genotypes is shown below: Name of Clone Genotypes 94CY017.41 A/? 94IN476.104 C 96ZM651.8 C 96ZM751.3 C 93BR020.1 F 90CF056.1 H 92R W009.6 A/C 92NG083.2 A/G 92NG003.1 A/G 93BR029.4 B/F 94CY032.3 A/G/I

[0145] For those sequences representing recombinant members of HIV-1, a variety of phylogenetic methods were used to further characterize the subtype composition.

[0146] The multiple computer-generated alignments of nucleotide sequences are shown in FIGS. 13A-13Z. The multiple computer-generated alignments of encoded amino acid sequences are shown in FIGS. 14-22. These alignments serve to highlight regions of homology and non-homology between different sequences and hence, can be used by one skilled in the art to design oligonucleotides and polypeptides useful as reagents in diagnostic assays for HIV-1.

[0147] The following examples illustrate certain embodiments of the present invention, but should not be construed as limiting its scope in any way. Certain modifications and variations will be apparent to those skilled in the art from the teachings of the forgoing disclosure and the following examples, and these are intended to be encompassed by the spirit and scope of the invention.

EXAMPLE 1

[0148] Materials and Methods

[0149] Virus Isolates

[0150] All viruses used were propagated in normal donor peripheral blood mononuclear cells (PBMCs) and thus represent primary isolates. Their biological phenotype (SI/NSI), year of isolation, relevant epidemiological and clinical information, as well as appropriate references are summarized in Table 1. For consistency, isolates are labeled according to WHO nomenclature (28). Preliminary subtype classification was made on the basis of partial env and/or gag gene sequences (1,17,19,43).

[0151] Amplification of Near Complete HIV-1 Genomes Using Long PCR Methods

[0152] (Near) full length HIV-1 genomes were amplified from short-term cultured PBMC DNA essentially as described (18,56) using the GeneAmp XL kit (Perkin Elmer Cetus, Foster City, Calif.) and primers spanning the tRNA primer binding site (upstream primer UPIA: 5′-AGTGGCGCCCGAACAGG-3′) (SEQ ID NO: 109) and the R/U5 junction in the 3′ long terminal repeat (downstream primer Low2: 5′-TGAGGCTTAAGCAGTGGGTTTC-3′) (SEQ ID NO: 110). Some isolates were amplified with primers containing Mlu1 restriction enzyme sites to facilitate subsequent subcloning into plasmid vectors (upstream primer UP1AMlu1: 5′-TCTCTacgcgtGGCGCCCGAACAGGGAC-3′ (SEQ ID NO: 111); downstream primer Low1Mlu1: 5′-ACCAGacgcgtACAACAGACGGGCACACACTA-CTT-3′ (SEQ ID NO: 112); lower case letters indicate the Mlu1 restriction site). Whenever possible, PBMC DNAs were diluted prior to PCR analysis to attempt amplification from single proviral templates. Cycling conditions included a hot start (94° C., 2 min), followed by 20 cycles of denaturation (94° C.; 30 sec) and extension (68° C.; 10 min), followed by 17 cycles of denaturation (94° C.; 30 sec) and extension (68° C., 10 min) with 15 second increments per cycle. PCR products were visualized by agarose gel electrophoresis and subcloned into pCRII by T/A overhang or following cleavage with Mlu1 into a modified pTZ18 vector (pTZ18Mlu1) containing a unique Mlu1 site in its polylinker. Transformations were performed in INVαF′ cells, and colonies were screened by restriction enzyme digestion for full length inserts (transformation efficiencies were generally poor, yielding only a few recombinant colonies; however, once subcloned, full length genomes were stable in their respective vectors). One full length clone per isolate was randomly chosen for subsequent sequence analysis.

[0153] Construction of a Full Length and Infectious Molecular Clone of 94UG114.1

[0154] A 674 bp fragment spanning most of the viral LTR (lacking 1-92 of U3 sequences) as well as the untranslated leader sequence preceding gag, was amplified from 94UG114 PBMC DNA, using primers and conditions described previously (18). After sequence confirmation, this LTR fragment was cloned into the pTZ18Mlu1 vector, which was subsequently cleaved with Nar1 (in the primer binding site) and Mlu1 (in the polylinker) to allow the insertion of the 94UG114.1 long PCR product cleaved with the same restriction enzymes. The resulting plasmid clone comprised a full length 94UG 114.1 genome with 3′ and 5′ LTR fragments containing all regulatory elements necessary for viral replication. A similar strategy could be used to construct replication competent genomes for all 11 clones reported in this application.

[0155] Sequence Analysis of HIV-1 Genomes

[0156] A number of the clones described herein were sequenced using the shotgun sequencing approach (37). Briefly, viral genomes were released from their respective plasmid vectors by cleavage with the appropriate restriction enzymes, purified by gel electrophoresis, and sonicated (Model XL2020 Sonicator; Heat System Inc., Framingdale, N.Y.) to generate randomly sheared DNA fragments 600-1,000 bp in length. Following purification by gel electrophoresis, fragments were end-repaired using T4 DNA polymerase and Klenow enzyme and ligated into SmaI digested and dephosphorylated M13 or pTZ18 vectors. Approximately 200 shotgun clones were sequenced for each viral genome using cycle sequencing and dye terminator methodologies on an automated DNA sequenator (Model 377A; Applied Biosystems, Inc.). Sequences were determined for both strands of DNA. Other clones were sequenced directly using the primer walking approach (primers were designed approximately every 300 bp along the genome for both strands). Proviral contigs were assembled from individual sequences using the SEQUENCHER program (Gene Codes Corporation, Ann Arbor, Mich.). Sequences were analyzed using EUGENE (Baylor College of Medicine, Houston, Tex.) and MASE (12).

[0157] Phylogenetic Tree Analysis

[0158] Phylogenetic relationships of the newly derived viruses were estimated from sequence comparisons with previously reported representatives of HIV-1 group M (45). Multiple gag and env sequence alignments were obtained from the Los Alamos sequence database (http://hiv-web.lan1.gov/HTML/alignments.html). Newly derived gag and env sequences were added to these alignments using the CLUSTAL W profile alignment option (67) and adjusted manually using the alignment editor MASE (12). All partial sequences were removed from these alignments. Sites where there was a gap in any of the remaining sequences, as well as areas of uncertain alignment, were excluded from all sequence comparisons. Pairwise evolutionary distances were estimated using Kimura's two parameter method to correct for superimposed substitutions (26). Phylogenetic trees were constructed using the neighbor-joining method (55), and the reliability of topologies was estimated by performing bootstrap analysis using 1,000 replicates (13). NJPLOT was used to draw trees for illustrations (49). Phylogenetic relationships were also determined using maximum-parsimony (with repeated randomized input orders; ten iterations) as well as maximum-likelihood approaches, implemented using the programs DNAPARS and DNAML from the PHYLIP package (14).

[0159] Complete Genome Alignment

[0160] All newly derived HIV-1 genome sequences were aligned with previously reported (45) full length representatives of HIV-1 subtype A (U445), B (LAI, RF, OYI, MN, SF2), C (C2220), D (ELI, NDK, Z2Z6), and “E” (90CF402.1, 93TH253.3, CM240) as well as SIVcpzGAB as an outgroup using the CLUSTAL W (67) profile alignment option (the alignment includes the untranslated leader sequence, gag, pol, vif, vpr, tat, rev, vpu, env, nef and available 3′ LTR sequences). Sequences that needed to be excluded from any particular analysis were removed only after gap-tossing was performed on the complete alignment containing all sequences. This ensured that all positions were comparable in different runs with different sequences.

[0161] Diversity Plots

[0162] The percent diversity between selected pairs of sequences was determined by moving a window of 500 bp in 10 bp increments along the genome alignment. The divergence values for each pairwise comparison were plotted at the midpoint of the 500 bp segment.

[0163] Bootstrap Plots

[0164] Bootscanning was performed on neighbor-joining trees using SEQBOOT, DNADIST (using Kimura's correction), NEIGHBOR and CONSENSUS from the PHYLIP package (14) for a window of 500 bp moved along the alignment in increments of 10 bp. 1000 replicates were evaluated for each phylogeny. The program ANALYZE from the bootscanning package (57) was used to examine the clustering of the putative hybrid with representatives of the subtypes presumed to have been involved in the recombination event. The bootstrap values for these sequences were plotted at the midpoint of each window.

[0165] Exploratory Tree Analysis

[0166] Exploratory tree analysis was performed using the bootstrap plot approach described above, except in this case an increment of 100 bp was used and each neighbor-joining tree was viewed using DRAWTREE from the PHYLIP package (14). In addition, all full length sequences (except known recombinants) were included into the analysis.

[0167] Informative Site Analysis

[0168] To estimate the location and significance of cross-overs, each putative hybrid sequence was compared with a representative of each of the two subtypes inferred to have been involved in the recombination event, and an appropriate outgroup. Recombination breakpoints were mapped by examining the linear distribution of phylogenetically informative sites supporting the clustering of the hybrid with each of the two “parental” subtypes, essentially as described (52,53). Potential breakpoints were inserted between each pair of adjacent informative sites, and the extent of heterogeneity between the two sides of the breakpoint, with respect to numbers of the two kinds of informative site, was calculated as a 2×2 chi square value; the likely breakpoint was identified as that which gave the maximal chi-square value. Since the alignments contained more than one putative cross-over, this analysis was performed looking for one and two breakpoints at a time, and repeated on subsections of the alignment defined by breakpoints already identified. To assess the probability of obtaining (by chance) chi-square values as high as those observed, 10,000 random permutations of the informative sites were examined.

[0169] Nucleotide Sequence Accession Numbers

[0170] GenBank accession numbers for several of the (near) full length HIV-1 proviral sequences disclosed in this application are listed in Table 2, and are hereby incorporated by reference.

EXAMPLE 2

[0171] Identification of Non-Subtype B HIV-1 Viruses

[0172] Molecular Cloning of Non-Subtype B HIV-1 Isolates

[0173] Of the geographically diverse HIV-1 isolates described herein, five had previously been classified as members of (group M) subtypes A (92RW009), F (92BR020, 92BR029), and G (92NG003, 92NG083) on the basis of env (17,19) and/or gag sequences (1). One (90CF056) was chosen because it originated from a major epicenter of the African AIDS epidemic. In addition, 90CF056 did not fall into any known subtype at the time of its first genetic characterization (43). Isolates from Zambia (96ZM651 and 96ZM75 1) and India (94IN476) were chosen because of the known subtype C prevalence in those countries. The two isolates from Cyprus (94CY017 and 94CY032) were selected because of the extensive diversity of HIV-1 in the drug user population (29). Table 1 summarizes available demographic and clinical information, as well as biological data concerning the isolate phenotype (SI/NSI). Only viruses grown in normal donor PBMCs were selected for analysis. TABLE 1 Epidemiological and clinical information for study isolates Preliminary Risk Disease Antiviral Year of^(d) Biological subtype Isolate^(a) Sex^(b) Age City Country factor^(c) status^(d) therapy isolation Source^(e) phenotype^(l) assignment Refs. 94CY017.41 F 35 Nicosia Cyprus Het SM n/a 1994 ADARC n/a A/? 29 94CY032.3 M 35 Nicosia Cyprus Ret AS n/a 1994 ADARC n/a G/A/I 29 96ZM651.8 M 47 Lusaka Zambia Het SM n/a 1996 UAB n/a n/a n/a 96ZM751.3 M 26 Lusaka Zambia Het SM No 1996 UAB n/a n/a n/a 94IN476.104 F n/a Pune India n/a n/a No 1994 ADARC n/a n/a n/a 93BR020 M 52 Rio de Janeiro Brazil Bi AS No 1993 WHO SI F 19, 72 90CF056 M n/a Bangui CAR Het AS No 1990 PIB NSI U 43 (U4056) 92RW009 F 24 Kigali Rwanda Het AS No 1992 WHO NSI A^(h) 17, 72 93BR029 M 17 Sao Paulo Brazil n/a AS No 1993 WHO NSI F^(h) 19, 72 92NG083 F 27 Jos Nigeria n/a AIDS No 1992 IHV NSI G^(h)  1 (JV1083) 92NG003 F 24 Jos Nigeria Het AS n/a 1992 IHV NSI G^(h)  1 (G3)

[0174] The viral genomes were cloned by long PCR methods using primers homologous to the tRNA primer binding site (upstream primer) and the polyadenylation signal in the 3′ LTR (downstream primer). This amplification strategy generated (near) full length genomes containing all coding and regulatory regions, except for 70 to 80 bps of 5′ unique LTR sequences (U5). All isolates, regardless of subtype classification, yielded long PCR products with the same set of primer pairs. In some instances, genomes were amplified with primers containing Mlu1 restriction enzyme sites. This greatly facilitated subsequent subcloning into a plasmid vector (Table 2).

[0175] Sequence Analysis of (Near) Full Length HIV-1 Genomes

[0176] All eleven HIV-1 genomes were sequenced in their entirety using either shotgun sequencing or primer walking approaches. The long PCR derived clones ranged in size from 8,952 to 8,999 base pairs, and spanned the genome from the primer binding site to the R/U5 junction of the 3′ LTR. Inspection of potential coding regions revealed that all clones contained the expected reading frames for gag, pol, vif, vpr, tat, rev, vpu, env and nef. In addition, all major regulatory sequences, including promotor and enhancer elements in the LTR, the packaging signal, splice sites, etc., appeared to be intact. None of the genomes had major deletions or rearrangements, although inspection of the deduced protein sequences identified inactivating mutations in seven of the eleven clones (Table 2). However, most of these were limited to point mutations in single genes and were thus amenable to repair. Only two genomes (92NG003.1 and 92NG083.2) contained stop codons, small deletions and frameshift mutations in several genes, rendering them multiply defective. Importantly, no inactivating mutations were identified in 93BR020.1 (subtype F), 90CF056.1 (subtype H), and 96ZM651.8 (subtype C), suggesting that these clones encoded biologically active genomes (Table 2). Nucleic acids containing repaired coding sequences, as well as the polypeptides encoded by the repaired coding sequences, are also considered to be a part of the invention. TABLE 2 Inactivating mutations in near-complete HIV-1 genomes Defective Inframe stop Frameshift Altered Plasmid GenBank Clone gene(s) codon^(a) mutation^(a) initiation codon^(a) vector^(d) accession number 93BR020.1 none — — — pCR2.1 AF005494 90CF056.1 none — — — pCR2.1 AF005496 92RW009.6 gag —  213 — pTZ18 (Mlu1) U88823 93BR029.4 gag — 260, 472 — pTZ18 (Mlu1) AF005495 92NG083.2 gag, vpu  360  5462^(b)  157 pTZ18 (Mlu1) U88826 92NG003.1^(c) vpr, vpu, nef — 5024^(b) ,5485^(b) 8113 pTZ18 (Mlu1) U88825 96ZM651.8 none — — — pTZ18 (Mlu1) pending 96ZM751.3 gag/pol/env 7567 1067/2688 — pTZ18 (Mlu1) pending 94IN476.104 pol/vpr 3021 — — pTZ18 (Mlu1) pending 94CY032.3 vif/env/vpr 4518/7125 5199 — pTZ18 (Mlu1) pending 94CY017.41 rev — — 5327 pCRII pending

EXAMPLE 3

[0177] Phylogenetic Analyses in Gag and Env Regions

[0178] To determine the phylogenetic relationships of the viruses described herein, evolutionary trees from full length gag and env sequences were first constructed. This was done to confirm the authenticity of previously characterized strains, classify the new viruses, and compare viral branching orders in trees from two genomic regions. The results confirmed a broad subtype representation among the selected viruses (FIGS. 1A-1B). Strains fell into six of the seven major (non-B) clades, including three for which full length sequences are not available (i.e., F, G and H). However, comparison of the gag and env topologies also identified three strains with discordant branching orders. 92RW009.6 grouped with subtype C viruses in gag, but with subtype A viruses in env. Similarly, 93BR029.4 clustered with subtype B viruses in gag, but with subtype F viruses in env. 94CY017.41 appeared to cluster within subtype A viruses in env, but fell into an unknown subtype in gag. However, characterization of the latter strain is still ongoing. These different phylogenetic positions were supported by high bootstrap values and thus indicated that these strains were intersubtype recombinants.

EXAMPLE 4

[0179] Diversity Plots

[0180] To characterize the putative recombinants as well as the other strains in regions outside gag and env, pairwise sequence comparisons with available full length sequences from the database were performed. A multiple genome alignment was generated which included the new sequences as well as U455 (subtype A), LAI, RF, OYI, MN and SF2 (subtype B), C2220 (subtype C), ELI, NDK and Z2Z6 (subtype D), and 90CF402.1, 93TH253.3 and CM240 (“subtype E”). The percent nucleotide sequence diversity between sequence pairs was then calculated for a window of 500 bp moved in steps of 10 bp along the alignment. Importantly, distance values were calculated only after all sites with a gap in any of the sequences were removed from the alignment. This ensured that all comparisons were made across the same sites.

[0181] FIGS. 2A-2J depict selected distance plots for the newly characterized viruses. For example in FIG. 2A, 93BR020.1 (putative subtype F) is compared to U455 (subtype A), NDK (subtype D), C2220 (subtype C) and 90CF056.1 (putative subtype H). The resulting plots all exhibit very similar diversity profiles characterized by alternating regions of sequence variability and conservation (values range from 7% divergence near the 5′ and 3′ ends of pol, to 30% in the segment of env encoding the V3 region). Moreover, the four plots are virtually superimposable, indicating that 92BR020.1 is roughly equidistant from U455, NDK, C2220 and 90CF056.1 over the entire length of its genome. A very similar set of distance curves was also obtained from comparisons of 94CY017.41 with 90CF056.1, 92BR025.8, 93BR020.1, U455, and NDK (FIG. 2B), and from comparisons of both 93BR020.1 and 90CF056.1 with representatives of subtype B and “E” (data not shown). These results indicating that 93BR020.1 and 90CF056.1 are equidistant from each other as well as from members of subtypes A, B, C, D and “E”, together with the gag and env phylogenetic trees (FIGS. 1A-1B), suggest that 93BR020.1 and 90CF056.1 represent non-recombinant members of subtypes F and H, respectively.

[0182] Very similar data were also obtained when 90CF056.1 was subjected to diversity plot analysis using the same set of reference sequences (FIG. 2F). Again, distance curves exhibited very similar profiles indicating approximate equidistance among the strains analyzed, except when viruses from the same subtype were compared. For example, in FIG. 2C distances between 94IN476.104 (putative subtype C) and U455, 93BR020.1, 90CF056.1, NDK and 92BR025.8, respectively, are depicted. As expected, the 92BR025.8 (putative subtype C) plot falls clearly below all others, indicating the lower level of sequence divergence between viruses from the same subtype (ranging from about 4% in pol to about 17% in env). Importantly, however, inter- and intra- diversity plots follow each other very closely, i.e., the same genomic regions exhibit proportionally higher and lower levels of divergence. See also the diversity plot analysis for 92ZM651.8 (FIG. 2G) and 96ZM751.3 (FIG. 2H). Thus, both at the level of inter- and intra-subtype comparisons, there was no evidence of mosaicism in the genomes of these three viruses. Together with the results in FIG. 1, this suggests that strains 94IN476.104, 96ZM651.8 and 96ZM751.3 represent non-mosaic members of subtype C.

[0183] By contrast, the diversity plots of the putative recombinants 92RW009.6 (FIG. 2D) and 93BR029.4 (FIG. 21) exhibited disproportionate levels of sequence divergence from different subtypes along their genome, consistent with their discordant branching orders in gag and env trees. As shown in FIG. 2D, 92RW009.6 is most similar to the subtype C strain C2220 in the 5′ half of gag, most of pol, vif, vpr, as well as nef (the C2220 curve falls below all others). However, in the 3′ end of gag, the 5′ end of pol, and most of env, 92RW009.6 is most similar to the subtype A strain U455 (the U455 curve falls below all others). Similarly in FIG. 21, 93BR029.4 is most similar to the subtype B strain LAI in gag, pol and vpr, while it is most similar to the putative subtype F strain 93BR020.1 in vif, env and nef regions. In each case, the magnitude of the difference between the new sequence and the most similar subtype was no greater than the diversity seen within subtypes. Thus, these data suggest that 92RW009.6 and 93BR029.1 represent mosaics, comprised of subtypes A/C and B/F, respectively. In each case, the plots suggested several (at least four) cross-overs; these are the minimum number of recombination breakpoints, since the window size used makes it unlikely that recombinant regions shorter than 500 bp would be detected.

[0184] Finally, inspection of the diversity plots for 92NG003.1 (FIG. 2J) and 92NG083.2 (FIG. 2E) also revealed disproportionate levels of sequence variation, although not as pronounced as for 92RW009.6 and 93BR029.4. Isolates 92NG003.1 and 92NG083.2 are equidistant from members of subtypes A-F and H for the most part of their genome, suggesting that they represent an independent subtype, i.e., subtype G. However, in the vif/vpr region the U455 distance plot falls below all others, suggesting a disproportionately closer relationship to subtype A. Assuming that U455 is non-mosaic, these results suggest that both 92NG003.1 and 92NG083.2 contain short fragments of subtype A sequence in the central region of their genome.

EXAMPLE 5

[0185] Exploratory Tree Analyses

[0186] To examine the phylogenetic position of the newly derived strains relative to each other and to the reference sequences over the entire genome, exploratory tree analyses were performed using the same multiple genome alignment generated for the diversity plots (FIGS. 3A-31). A total of 79 trees were constructed for overlapping fragments of 500 bp, moved in 100 bp increments along the alignment. As expected, four genomes were identified that clustered in different subtypes in different parts of their genome. These included 93BR029.4 which alternated between subtypes F and B, 92RW009.6 which alternated between subtypes A and C, and 92NG083.2 and 92NG003.1 which grouped either independently or within subtype A. Interestingly, the latter two strains exhibited distinct patterns of mosaicism. In trees spanning the region 3501-4000, 92NG003.1 clustered within subtype A, while 92NG083.2 clustered independently, presumably representing subtype G. In contrast to these strains, there was no evidence for a hybrid genome structure in 94IN476.104, 96ZM651.8, 96ZM751.3, 93BR020.1 or 90CF056.1. These viruses branched consistently in all regions analyzed. Based on these findings and the results from the diversity plots, it appeared that five of the eleven selected HIV-1 strains represent non-recombinant reference strains for subtypes C (94IN476.104, 96ZM651.8, 96ZM751.3), F (93BR020.1) and H (90CF056.1), respectively, while at least five are intersubtype recombinants. CYO 17.41 may be recombinant, but work is in progress in this regard.

EXAMPLE 6

[0187] Recombination Breakpoint Analysis

[0188] To map the location of the recombination breakpoints in 92RW009.6 and 93BR029.4, bootstrap plots and informative site analyses were used (18,52,53). Unrooted trees were constructed which included U455, 92UG037.1, LAI, MN, OYI, SF2, RF, C2220, 92BR025.1, NDK, ELI, Z2Z6, 93BR020.1 and 90CF056.1; then the magnitude of the bootstrap values supporting (i) the clustering of 92RW009.6 with members of subtype A (U455, 92UG037.1) or C (2220, 92BR025.8), as well as (ii) the clustering of 93BR029.4 with members of subtype B (LAI, MN, OYI, MN, RF) or F (92BR020. 1) was determined (in the latter case subtype D viruses were excluded because of their known close relationship to subtype B viruses). FIGS. 4A-4B depict the results of 797 such phylogenetic analyses generated for each genome, performed on a window of 500 nucleotides moved in steps of 10 nucleotides. Very high bootstrap values (>80%) supporting the clustering of 92RW009.6 with subtype C were apparent in gag, the 3′ two-thirds of pol, and nef. By contrast, significant branching of 92RW009.6 with subtype A was apparent in the gag/pol overlap and the env region. In a small region (4,000 to 4,200) in the middle of the genome, 92RW009.6 appeared not to cluster significantly with either subtype, but further inspection revealed that this was due to a small number of informative sites. These data thus indicated four points of recombination crossovers between subtypes A and C (FIG. 4A). A similar analysis identified six recombination breakpoints between subtypes B and F in 93BR029.4 (FIG. 4B). These included two more (in gag) than were apparent from the diversity plot analysis (compare FIGS. 2A-2J), indicating a greater sensitivity of this approach.

[0189] To map the recombination cross-over points in 92RW009.6 and 93BR029.1 more precisely, the distribution of phylogenetically informative sites supporting alternative tree topologies were examined (52,53). Briefly, this was done in a four sequence alignment which included the query sequence, a representative of each of the two subtypes presumed to have been involved in the recombination event, and an outgroup. Breakpoints were identified by looking for statistically significant differences in the ratios of sites supporting one topology versus another. Consistent with the bootscanning data, this analysis identified four breakpoints in 92RW009.6, and six in 93BR029.4 (Table 3). A schematic representation of the mosaic genomes of 92RW009.6 and 93BR029.4 is depicted in FIG. 6. TABLE 3 Informative site analysis of 92RW009.6 and 93BR029.4 Informative Sites subtype A subtype C outgroup Clone Region^(#) Subtype (U455) (C2220) (NDK) 92RW009.6   1-1037 C  8  32  8 1085-1940 A 17  5  4 1986-5288 C 18  99 27 5293-7238 A 60  9 13 7254-8431 C 12  55 12 subtype B subtype F outgroup (LAI) (93BR020) (C2220) 93BR029.4  1-735 B 18  6  3 755-896 F  1  10  0  930-4247 B 99  10 14 4340-4668 F  2  15  1 4787-5166 B 15  0  5 5244-8242 F 15 139 13 8250-8429 B 13  0  0 # the alignment.

[0190] Numbers mark positions in the four sequence alignment which includes the untranslated leader sequence (1-120), gag (121-1537), pol (1370-4340), vif (4285-4856), vpr (4799-5073), the first tat exon (5054-5271), vpu (5276-5488), env (5406-7726), nef (7727-8313) and the 3′ LTR (7991-8468). Note that position 8468 does not correspond to the end of the LTR but is the last position in the alignment after gaps have been tossed. The 5′ LTR is not included in the alignment. 10

[0191] Because of the lack of a full length subtype G reference sequence, recombination breakpoint analysis of 92NG003.1 and 92NG083.2 required a different approach. The analyses summarized in FIGS. 2A-2J and FIGS. 3A-3I suggested that these two viruses contained subtype A sequences in the middle of their genome. To attempt to confirm this, and to define the extent of these putative subtype A fragments, a more detailed diversity plot analysis of the viral middle region (between position 3,000 and 6,000) was performed using different viral strains and varying window sizes (ranging from 200 to 400 bp) to examine the extent of sequence divergence of 92NG083.2 and 92NG003.1 from members of other subtypes, including subtype A. Diversity plots for 92NG003.1 compared to U455, C2220, NDK and 92NG083.2 and for 92NG083.2 compared to U455, C2220, NDK and 92NG003.1 depicted representative results (using a window size of 300 bp moved in steps of 10 bp along the alignment) (data not shown). Similar to the data shown in FIGS. 2A-2J, the two “subtype G” viruses are roughly equidistantly related to members of subtypes A (U455), C (C2220), and D (NDK), except for two regions in 92NG003.1 and one region in 92NG083.2 where both viruses are disproportionately more closely related to U455 than they are to each other. Noting the points at which the “G”-A distance increases or decreases relative to the others allowed the tentative identification of recombination breakpoints. For example, at position 3400, the U455 plot falls whereas the C2220, NDK and 92NG083.2 plots do not, and around site 3600 the U455 plot crosses the 92NG083.2 plot. Bearing in mind the window size of 300 nucleotides, this finding suggested that a recombination cross-over occurred around position 3500. Similar “G”-A plot crossings around positions 3800, 4200 and 5200 (in the diversity plot for 92NG003.1), and around positions 4200 and 4800 (in the diversity plot for 92NG083.2), suggested additional recombination breakpoints.

[0192] Phylogenetic trees were then constructed using the regions of sequence defined by these putative breakpoints (FIGS. 5A-5C). This analysis generally supported the conclusions drawn from the diversity plots, i.e., 92NG003.1 clustered with subtype A viruses in the region between 3501 and 3800, whereas 92NG083.2 did not; and both 92NG003.1 and 92NG083.2 clustered with subtype A viruses in the region 4201 and 4800. However, neither the diversity plot nor the tree analysis allowed the definition of the boundaries of the subtype A fragments with certainty. Nevertheless, the data indicated that (i) both 92NG083.2 and 92NG003.1 represent G/A recombinants, (ii) that they are the result of different recombination events because some of their breakpoints are clearly different, and (iii) that 92NG083.2 likely encodes a non-recombinant pol gene. A schematic representation of the mosaic genomes of 92NG083.2 and 92NG003.1 is shown in FIG. 6.

EXAMPLE 7

[0193] Subtype Specific Genome Features

[0194] Having classified the new viruses with respect to their subtype assignments, their sequences were examined for clade-specific signature sequences. Comparing deduced amino acid sequences gene by gene, several subtype specific features were found (FIGS. 7A-7C). For example, most subtype D viruses contain an in-frame stop codon in the second exon of tat, which removes 13 to 16 amino acids from the carboxy terminus of the Tat protein (FIG. 7A). Similarly, all subtype C viruses (including 94IN476.104, 96ZM651.8 and 96ZM751.3) contain a stop codon in the second exon of rev which would be predicted to shorten this protein by 16 amino acids (FIG. 7B). Subtype C viruses also contain a 15 base pair insertion at the 5′ end of the vpu gene (FIG. 7C) which extends the putative membrane spanning domain of the Vpu protein by 5 amino acids (data not shown). Although these changes are unlikely to alter the function of the respective gene products in a major way (e.g., the known functional domains of both Tat and Rev proteins are not affected by these changes), it is possible that they could influence their mechanism of action in a subtle (but nevertheless biologically important) manner.

[0195] Of the eleven non-subtype B clones identified herein, phylogenetic analysis identifies five of these viruses as non-recombinant members of subtypes C (three), F and H, which increases the number of non-subtype B reference strains available. Among these, the (near) full length genomes of 93BR020.1 and 90CF056.1 represent the first such strains for subtypes F and H, respectively. Five of the other viruses were found to represent complex mosaics of subtypes A and C, A and G (two), B and F and A, G and I. One, 94CY017.41, is not yet fully characterized. Both A/G recombinants originated from Nigeria,.but must have arisen from independent recombination events since they are not closely related and differ in their patterns of mosaicism. One of these (92NG083.2) appears to contain only a single short (perhaps 600bp) segment of subtype A origin in the vif/vpr region, and in the absence of (as yet) any full length subtype G virus, thus serves as a (non-mosaic) subtype G representative for gag, pol, env, and nef regions. Importantly, the genomes were generated in such a way that they can be tested for biological activity following a simple reconstruction step. An example of such a reconstructed genome giving rise to replication competent virus (94UG114.1) demonstrates that this approach is feasible. See “Materials and Methods,” supra, and the schematic diagram in FIG. 8.

[0196] Given the apparent prevalence of mosaic viruses, it is clear that subtype specific reference strains can only be defined as such after comprehensive recombination analysis. Small subgenomic fragments or even full length gag and env sequences are not sufficient to identify all hybrid genomes. Although multiple cross-overs are a characteristic feature of retroviral recombination and have been found in many of the mosaic HIV-1 genomes examined (7,19,53,60,62), the examples of 92NG003.1 and 92NG083.2 demonstrate that cross-overs may be confined to regions outside of gag and env. Thus, elimination of the possibility that a virus is recombinant requires the determination of substantial (if not all) portions of its genome. As a consequence, subtype specific reference reagents, such as immunogens for cross-clade CTL and neutralization assays, should be derived from viral isolates for which a complete genome has been characterized.

[0197] These considerations emphasize the need for detailed analyses using reliable methods for identification of recombinant viral sequences. The above results indicate that diversity plots, depicting the distance between the query sequence and a set of reference sequences in moving windows along the genome, represent an excellent initial screening tool. The extent of sequence divergence (between any pair of viruses) varies along the genome, but since all plots are shown in the same graph, particular regions where the query sequence is anomalously highly similar to (or divergent from) other sequences can be readily identified. For example, this approach uncovered the subtype A-like regions in the middle of the putative “subtype G” genomes 92NG003.1 and 92NG083.2 (FIGS. 2J and 2E; FIGS. 5A-5C). However, the results from such analyses relying only on extents of sequence divergence must be treated with some caution, because they are susceptible to variation in evolutionary rate in different lineages. Once suspicious regions have been identified, phylogenetic analyses of windows of sequence around these regions can be used to look for discordant branching orders, and to identify the subtypes likely to have been involved in the recombination event. The bootstrap value supporting the clustering of the query sequence with sequences of the supposed “parental” subtypes can be examined, again in moving windows along the genome. Finally, informative site analysis can be used to map as precisely as possible the breakpoints of the putative recombination events (52,53).

[0198] Clearly, recombination analysis relies on the availability of accurately defined non-mosaic reference sequences. Thus, location of the breakpoints in the two G/A recombinant viruses identified here must remain tentative because of the lack of such reference sequences for subtype G. The precise positions of breakpoints in the recently characterized Thai and CAR “subtype E” viruses are similarly uncertain (7,18), in this case for lack of a complete non-mosaic subtype E reference sequence. It should also be emphasized that currently designated reference sequences may require revision in the future. For example, the inadvertent inclusion of recombinant “reference” sequences in previous tree analyses (19,40) led to an incorrect subtype assignment of subtype G and “E” gp41 sequences. As more sequences become available, it is thus possible that one or more of the viral sequences currently designated as non-recombinant may be identified as a hybrid.

EXAMPLE 8

[0199] Identification of the HIV-1 Clone 94CY032.3

[0200] Full length reference clones and sequences are currently available for eight HIV-1 group M subtypes (A-H), but none have been reported for subtypes I and J, which have only been identified in a handful of individuals. Phylogenetic information for subtype I, in particular, is limited since only a very small env gene fragment (400 bp in the C2-V3 region) obtained from only two individuals (a heterosexual couple of intravenous drug users from Cyprus) has been analyzed. To characterize subtype I in greater detail, long range PCR was employed to clone a full length provirus (94CY032.3) from a short-term cultured isolate (94CY032) established from one of the two individuals originally reported to be infected with this subtype.

[0201] Using primers homologous to the tRNA primer binding site (5′-TCTCT-acgcgtGGCGCCCGAACAGGGAC-3′ (SEQ ID NO: 111), lower case letters indicate an Mlu1 site) and the polyadenylation signal in the 3′ LTR (5′-ACCAGacgcgtACAACAGACGGG-CACACACTACTT-3′) (SEQ ID NO: 112), long range PCR was used to amplify near full length genomic fragments, which contained all coding and regulatory regions except for 102 bp of 5′ unique LTR sequences (U5) (for methodological details concerning the long range PCR approach see refs. 18, 56, 79). Amplification products were subcloned into an a plasmid vector, mapped by restriction enzyme digestion, and one clone (94CY032.3) was selected for further analysis. A 694 bp fragment spanning the remainder of the LTR was amplified separately using a semi-nested approach (18).

[0202] The complete sequence of 94CY032.3 was determined using the primer walking approach [GenBank accession numbers: AF049337 (genome) and AF049338 (LTR)]. Examination of potential coding regions revealed the expected reading frames for gag, pol, vif, vpr, tat, rev, vpu, env and nef (FIGS. 13A-13Z). None of the genes contained major deletions, insertions or rearrangements. However, both env and vif genes contained single in-frame stop codons (FIGS. 13A-13Z). There was also a frameshift at position 5199 (single base pair insertion) which altered the C-terminus (last six amino acid residues) of the Vpr protein. All other protein domains of known function as well as major regulatory sequences, including the primer binding site, the packaging signal and major splice sites, appeared to be intact. Similarly, the number, position and consensus sequences of promoter and enhancer elements in the 94CY032.3 LTR were indistinguishable from those of most other HIV-1 strains, except for the presence of an unusual TATA sequence (TAAAA), thus far only found in “subtype E” (A/E) viruses from Thailand and the Central African Republic (7, 18).

[0203] To compare 94CY032.3 to previously reported subtype I sequences, a phylogenetic tree was constructed from C2-V3 sequences, including representatives of all 10 known group M subtypes (data not shown). As expected, 94CY032.3 clustered most closely with CYHO321 and CYHO322, sequences amplified from uncultured PBMC DNA of the same individual (HO32) from whom the 94CY032 isolate was derived. 94CY032.3 also clustered very closely with CYHO3 11, a sequence derived from the sexual partner of HO32 (29), strongly suggesting that the two infections were epidemiologically linked. Finally, as observed in the past (29), all subtype I sequences clustered independently, forming a distinct lineage roughly equidistant from all other subtypes, including subtype J (30). These findings thus confirmed the authenticity of the 94CY032.3 clone and validated it as a representative of subtype I in the C2-V3 region of the viral envelope.

[0204] To characterize the remainder of the 94CY032.3 genome, pairwise sequence comparisons were then performed with recently reported non-mosaic reference sequences for subtypes A-H (32, 79) as well as selected intersubtype recombinants (83). This approach has been useful for identifying regions of unusual sequence similarity (or dissimilarity) as an indicator of recombination (18, 79). Briefly, 94CY032.3 was added (using the profile alignment option of CLUSTAL W; 27) to a multiple genome alignment which included a total of 28 sequences from the database (81) representing subtypes A (U455, 92UG037.1), B (LAI, RF, OYI, MN and SF2), C (C2220, 92BR025.8), D (NDK, Z2Z3, ELI, 84ZR085.1, 94UG114.1), F (93BR020.1), and H (90CF056.1) as well as A/C (ZAM184, 92RW009.6), A/G (92NG083.2, 92NG003.1, Z321, IBNG), A/D (MAL), and A/E (93TH253.3, CM240, 90CF402.1) and B/F (93BR029.4) recombinants (SIVcpzGAB was included as an outgroup). All sites with a gap in any of the sequences were removed from the alignment to ensure that all comparisons were made across the same sites. The percent nucleotide sequence diversity between 94CY032.3 and selected other viruses was then calculated for sequence pairs by moving a window of 400 bp in steps of 10 bp along the genome.

[0205]FIG. 9 depicts five such distance plots which illustrate the extent of sequence divergence of 94CY032.3 from representatives of subtypes A (92UG037.1), B (LAI), C (C2220), D (ELI) and G/(A) (92NG083.2). The analysis yielded a set of distance curves with very similar (and for the most part superimposable) diversity profiles, suggesting that 94CY032.3 was roughly equidistant from the other subtypes in most regions of its genome (the same results were also obtained when 94CY032.3 was compared to representatives of subtypes A/E, F, and H; data not shown). However, careful inspection of the graphs revealed several small areas of disproportionate sequence similarity involving two of the five reference sequences. For example, at the 3′ end of gag and the 3′ end of pol, 92NG083.3 dropped below all others, indicating a relative greater similarity of 94CY032.3 to subtype G. Similarly, in the 5′ end of gag, vif and the 3′ and 5′ end of env, 92UG037.1 fell below all others, indicating a relative greater similarity of 94CY032.3 to subtype A. Together, these results suggested that 94CY032.3 contained subtype A and G-like segments, in addition to regions that appeared to be equidistant from the other subtypes.

[0206] Relative differences in the extent of sequence similarity as determined by diversity plots (18, 79) or other methods of distance measurement (75) are not always an indicator of recombination, but can reflect variations in the evolutionary rates of the lineages compared. To determine whether 94CY032.3 was truly mosaic, an exploratory tree analysis was then performed to look for significantly discordant phylogenetic positions for different parts of its genome (FIGS. 10A-10K). Using the same multiple genome alignment described above, but excluding all known recombinants (except 92NG083.3 and 92NG003.1), unrooted trees were constructed for overlapping fragments of 400 bp, moved in 10 bp increments along the alignment (for subtypes B and D only three representatives were included). Inspection of the resulting topologies revealed that 94CY032.3 changed its phylogenetic position a total of ten times, alternating between subtype A (FIG. 10A, E, G and J; panels 201-600, 4241-4640, 5071-5470 and 6821-7220), subtype G (FIG. 10B, D and H; panels 1101-1500, 3841-4240 and 5471-5870), and an independent position (FIG. 10C, E, I and K; panels 1751-2150, 4641-5040, 5901-6300 and 7901-8300) that was very similar to the one observed in the C2-V3 region (all discordant positions were supported by significant bootstrap values). Since the latter has served as the basis for subtype I definition, it is most parsimonious to assume that all independently grouping segments in 94CY032.3 are of a common origin and thus represent “subtype I”. 94CY032.3 thus appears to be comprised of sequences belonging to at least three different (group M) subtypes.

[0207] To map the boundaries of the putative A, G and I segments, boostrap plot analyses were performed as previously described (18, 57, 79), plotting the magnitude of the bootstrap values that supported the clustering of 94CY032.3 with 92UG037.1 (subtype A), as well as that of 94CY032.3 with 92NG083.2 (“subtype G”). The results of these analyses allowed us to tentatively map the location and boundaries of the various subtype A an G segments along the 94CY032.3 genome (FIG. 11). Bearing in mind the window size of 400 nucleotides and considering only peaks of significant bootstrap values (>80%), we identified two A/G cross-overs around 1200 and 5600, and one G/A cross-over around 4100. The bootstrap plots also outlined regions with no peaks (or peaks below 80%), which coincided with segments that clustered independently (i.e., in subtype I) in the exploratory tree analysis. Delineating the boundaries of these regions suggested five additional breakpoints: G/I at 1500, I/G at 3800, G/I at 6000, I/A at 6900, and A/I at 7200. Because full length non-mosaic reference sequences for the parental lineages (G and I) were not available, most of the breakpoints could not be mapped with certainty (the A/G breakpoints at 1200 and 5600 were confirmed by informative site analysis; data not shown). Also, the recombinant nature of 92NG083.2 prohibited reliable breakpoint analysis between 4200 and 4800 (32, 79; highlighted in FIG. 11).

[0208] To map potential recombination breakpoints in this remaining region, four recently reported, partial but non-mosaic subtype G sequences from Mali which spanned the vif/vpr region and thus bridged the “subtype A gap” of 92NG083.2 were used (77). A set of distance plots that compare 94CY032.3 to one of these newly derived G sequences (95ML045) as well as representatives of subtype A (U455), B (MN), and D (ELI), respectively, were constructed (data not shown). Consistent with the results from the exploratory tree analysis (FIG. 4), 94CY032.3 was disproportionately more closely related to U455 in the 5′ and 3′ thirds of this fragment, suggesting the presence of subtype A-like segments. However, in the middle of the fragment, 94CY032.3 was clearly equidistant from U455 and the other subtypes, suggesting an independent position (diversity plots were generated for a window of 300 bp moved in increments of 10 bp). Thus, noting the points at which the “A” distance increased and decreased relative to the other distances allowed us to tentatively map the two remaining breakpoints, one at 4650 and the other at 5000. Trees constructed from sequences surrounding these two breakpoints (FIG. 12) confirmed that 94CY032.3 switched position from subtype A (FIG. 12; panel 4255-4650) to subtype I (panel 4651-5000), and back to subtype A (5001-5300; note, that the new subtype G sequences only cover the region between 4255 and 5300).

[0209] There are a total of 10 recombination breakpoints between the 5′ end of gag and the 3′ end of nef in the genome structure of the 94CY032.3. However, the discordant subtype assignments of gag and nef regions necessitate at least one more breakpoint in the viral LTR or the gag leader sequence (LTR sequences were not separately analyzed for mosaicism). Given this extent of mosaic complexity, 94CY032.3 is likely the result multiple sucessive recombination events.

[0210] Having identified several fragments of subtype I in 94CY032.3, evidence for its presence in other (full length) recombinants from the database was examined. (Data not shown) Two known mosaics MAL (53, 76) and Z321 (78) were of particular interest, because previous analyses had indicated that these viruses contain regions of uncertain subtype assignment (53, 82, 83). For example, MAL has long been known to represent a mosaic of subtypes A and D, but also contains a sizable pol fragment that has defied previous subtype classification (53, 83). Similarly, Z321 is a known mosaic .of subtypes A and G (78), but a recent re-analysis of its recombination breakpoints identified regions that could not be assigned to any known subtype (82, 83). To determine whether any of these regions represented subtype I, distance plot analysis was performed, comparing the diversity profiles of MAL and Z321 with those for representatives of other subtypes. Looking for dips in the curves as an indication of relatively greater sequence similarity, one in the pol region of MAL and another in the vif/vpr region of Z321 were found to coincide with previously unclassified segments of their genomes (indicated as white boxes). Phylogenetic tree analysis confirmed that these regions were indeed of subtype I origin, since MAL and Z321 clustered significantly with the subtype I domains of 94CY032.3. Interestingly, subtype I did not account for all of the unclassifiable regions in MAL and Z321 (82, 83). It thus remains unclear whether these represent still other, as yet unidentified, subtypes or regions of multiple breakpoints that cannot be mapped using current methods.

[0211] The above results demonstrate that a strain of HIV-1, proposed in 1995 as a prototypic “subtype I” isolate (29), represents a complex mosaic comprised of subtypes A, G and I, respectively. In addition, two of the oldest known isolates from Africa, MAL (isolated in 1984) (76) and Z321 (isolated in 1976) (80, 84), are shown to contain short segments of sequence closely related to the subtype I domains of 94CY032.3. These findings support the following conclusions: (i) although initially detected in Cyprus, subtype I must have existed in Africa as early as 1976; it is unknown whether full length non-mosaic representatives of subtype I still exist (but have not yet been sampled), or whether this subtype (like subtype E) is represented only by fragments in present day recombinants; (ii) the ancestry of 94CY032.3 must have involved multiple successive recombination events; it remains unclear whether this occurred in Africa and/or in Cyprus, where a number of different subtypes have also been documented (29); (iii) subtype I, along with subtypes A and G, must have diverged substantially earlier than the 1970s in order to be detectable as distinct segments in the Z321 genome; this is consistent with the recent molecular characterization of a virus from 1959 which in phylogenetic analyses appears to have postdated the group M radiation (85); (iv) finally, the finding of subtype I in several different recombinants, including one from an intravenous drug user (29), suggests that this subtype may be more widespread than previously thought, at least in the form of mosaic genome fragments. It will be interesting to screen additional viruses from drug user populations and their contacts in Cyprus and Greece to determine the current prevalence and geographic distribution of subtype I containing viruses.

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[0328] Modifications of the above described invention that are obvious to those of skill in the fields of genetic engineering, immunology, virology, protein chemistry, medicine, and related fields are intended to be within the scope of the following claims.

[0329] All of the references cited herein above are hereby incorporated by reference.

1 112 1 8968 DNA Human immunodeficiency virus type 1 isolate=93BR020; 133..1611gag; 4369.4947vif; 4887.5177vpr; 5158.7767tat; 5297.7957rev; 5396.5641vpu; 5559.8099env; 8101.8727nef 1 ctgaaagcga aagtaaacca gagaagaact ctcgacgcag gactcggctt gctgaagtgc 60 acacggcaag aggcgagagc ggcgactggt gagtacgcca aaatttgact agcagaggct 120 agaaggagag agatgggtgc gagagcgtca gtattaagcg ggggaaaatt agatgcttgg 180 gaaaaaattc ggttaaggcc ggggggaaag aaaaaatata gactaaaaca tctagtatgg 240 gcaagcaggg agctagaacg atttgcactt gatccaggcc ttctagaaac atcagaaggc 300 tgtcgaaaaa taataggaca gttacaacca tcccttcaga caggatcaga agagctcaaa 360 tcattatata atacaatagc agtcctctat tatgtacatc aaaaggtaga ggtaaaagac 420 accaaggagg ctttagagaa gctagaggaa gaacaaaaca aaggtcggca aaagacacag 480 caagcgactg ctgaaaaagg ggtcagtcaa aattacccta tagtacagaa tcttcaggga 540 caaatggtac accagtcttt atcacctaga actttaaatg catgggtaaa ggtgatagaa 600 gagaaggctt ttagtccaga agtaataccc atgttttcag cattatcaga aggggccact 660 ccacaagatt taaacaccat gttaaataca gtggggggac atcaagcagc catgcaaatg 720 ttaaaagaca ccatcaatga ggaggctgca gaatgggaca gattacatcc aacacaggca 780 ggacccatcc ccccaggtca gataagggaa cctaggggaa gtgatatagc tggaactact 840 agtacccttc aggaacaaat acaatggatg acaggcaacc cacctgtccc agtgggagaa 900 atgtataaaa gatggatcat cctaggatta aataaaatag taagaatgta tagccctgtc 960 ggcattttgg acataagaca agggccaaaa gaacccttta gagactatgt agacaggttc 1020 tttaaaaccc taagagctga gcaagctaca caggaagtaa agggttggat gacagacacc 1080 ttgttggtcc aaaatgcgaa cccagattgt aagaccattt taaaagcatt gggaccaggg 1140 gctacactag aggaaatgat gacagcatgt cagggagtgg gaggacctag ccataaggca 1200 agagttttgg ctgaggcaat gagccaagca acaaatacag ctataatgat gcagaaaagt 1260 aactttaagg gccaaagaag aattgttaaa tgctttaatt gtggcaaaga aggacacata 1320 gccaaaaatt gcagggcccc tagaaaaaag ggctgttgga agtgtggaag agagggacac 1380 caaatgaagg actgcactga gagacaggct aattttttag ggaaaatttg gccttccaac 1440 aaggggaggc ccggaaactt catccagaac aggccagagc cgtcagcccc gccagcagag 1500 agcttcaggt tcggggagga gacaacccca tctccgaagc aggagcagaa agacgaggga 1560 ctgtaccctc ccttagcttc cctcaaatca ctctttggca acgaccccta gtcacaataa 1620 gagtaggggg acagctaaag gaagctctat tagatacagg agcagatgat acagtattag 1680 aagacgtaaa tttgccagga aaatggaaac caaaaatgat agggggaatt ggaggtttta 1740 tcaaagtaaa acagtatgat agcatactca tagaaatttg tggacacaga gctataggta 1800 cagtgttagt aggacctacg cctgtcaaca taattggaag aaatatgttg acccagattg 1860 gttgtacttt acattttcca attagtccta ttgagactgt accagtaaaa ttgaagccag 1920 gaatggatgg cccaaaggtt aaacaatggc cattgacaga agaaaaaata aaagcattaa 1980 cagaaatatg tatggaaatg gaaaaggaag gaaaaatttc aaaaattggg cctgaaaatc 2040 catacaatac tccagtattt gccataaaga aaaaagacag tactaaatgg aggaaattag 2100 tagatttcag agaacttaat aaaagaactc aagatttttg ggaggttcaa ttaggaatac 2160 cgcatccagc agggttaaaa aagaaaaagt cagtaacagt actggatgtg ggggatgcat 2220 atttttcagt tcccttagat aaggatttca ggaagtacac tgcatccacc atacctagta 2280 ccaacaatga gacaccagga gttaggtacc agtacaatgt gcttccacaa ggatggaaag 2340 gatcaccagc aatattccaa tatagcatga caaaaatctt agatcccttt agagcaaaaa 2400 atccagacat agttatctac caatacatgg atgatttgta tgtagggtct gacttagaaa 2460 taggacagca tagaacaaaa atagaagagt taagagaaca tctactgaaa tggggattaa 2520 ctacaccaga caaaaaacat caaaaagaac ccccattcct ttggatgggg tatgaactcc 2580 atcctgataa atggacagtg cagcctatac aattgccaga caaggacagc tggactgtca 2640 atgatataca gaagttagta ggaaaactaa attgggcaag tcagatttat ccagggatta 2700 aagtaaaaca attatgtaaa ctccttaggg gagccaaggc actaacagac atagtgccac 2760 tgactacaga agcagagtta gaattggcag agaataggga gattctaaaa gaaccagtac 2820 atggggcata ttatgacccg tcaaaagact taatagcaga aatacagaaa caagggcaag 2880 ggcaatggac atatcaaatt tatcaagagc catttaaaaa tctaaaaaca ggaaagtatg 2940 caaaaatgag gtctgcccac actaatgatg taaaacagtt aacagaagca gtgcaaaaga 3000 tatctctaga aagcatagta atatggggca agactcctaa gtttagacta cccatattaa 3060 aagagacatg ggatacatgg tggacagagt actggcaagc cacctggatt cctgagtggg 3120 agtttgtcaa taccccccct ctagtaaaac tatggtatca gttagaaaca gagcccatag 3180 taggagcaga aaccttctat gtagatgggg catctaatag agagaccaaa aaaggaaaag 3240 caggatatgt tactgacaga ggaagacaaa aagcggtctc cctaactgag actacaaatc 3300 agaaggctga gttacaagca attcagttag ctttacagga ttcaggatca gaagtaaaca 3360 tagtaacaga ctcacagtat gcattaggaa tcattcaagc acaaccagat aagagtgaat 3420 cagagttagt caatcaaata atagagcaat taataaaaaa ggaaaaggtc tacctgtcat 3480 gggtaccagc acacaaaggg attggaggaa atgaacaagt agataaatta gtcagtgctg 3540 gaatcaggaa agtactgttt ctagatggga tagataaggc acaagaggaa catgaaaaat 3600 atcacaacaa ttggagagca atggctagtg attttaatat accagctgta gtagcaaaag 3660 aaatagtagc tagctgtgat aaatgtcagc taaaagggga agccatgcat ggacaagtag 3720 attgtagccc agggatatgg caattagatt gcacacattt agaaggaaaa attatcctgg 3780 tagcagtcca tgtagctagt gggtacctag aagcagaagt tatcccagca gaaacaggac 3840 aagagacagc ctacttccta ctaaagttag caggaagatg gccagtaaaa acaatacata 3900 cagacaatgg caccaatttc accagtgcca cggttaaggc agcttgttgg tgggcaggta 3960 tccagcagga atttggaatt ccttacaacc cccaaagtca aggagtagta gaatctatga 4020 ataaagagct aaagaaaatc ataggacaga taagagatca agctgaacat cttaagacag 4080 cagtccaaat ggcagtattc attcacaatt ttaaaagaaa aggggggatt gggggataca 4140 gtgcagggga aagaacaata gacataatag caacagacat acaaactaga gaattacaaa 4200 aacaaattat aaaaattcaa aatttccggg tttattacag ggacagcaga gacccagttt 4260 ggaaaggacc agcaaagcta ctctggaaag gtgaaggggc agtagtcata caagacaata 4320 gtgaaataaa ggtagttcca agaagaaaag caaagatcat tagggattat ggaaaacaga 4380 tggcaggtga tgattgtgtg gcaggtagac aggatgagga ttaacacatg gaaaagttta 4440 gtaaaatacc atatgcatat ttcaaagaaa gccaaaggat ggttttatag acatcacttt 4500 gaaagcaggc atccaaaaat aagttcagaa gtacacatcc cactagagac agctgaatta 4560 gtaataacaa catactgggg gctgcttcca ggagaaagag aatggcatct gggtcaggga 4620 gtctccatag aatggaggca ggggaggtat agaacacaaa tagaccctgg cctggcagac 4680 caactgatcc atatatatta ttttgattgt ttttcagaat ctgccataag gaaagccata 4740 ttaggacata aaattagccc taggtgtaac tatcaagcag gacataacaa ggtaggatct 4800 ctacaatact tggcactaac agcattaata gctccaaaaa agacaaagcc gcctttgcct 4860 agtgtccaga aactagtaga agacagatgg aacaagcccc agaagaccag gggccacaga 4920 gagagccata caatgaatgg acactagatc ttttagagga gcttaagaat gaagctgtta 4980 gacattttcc taggccatgg ctccatagct taggacaaca tatctataac acctatgggg 5040 atacttggga aggagttgaa gcaatcataa ggatattgca acaactactg tttatccatt 5100 tcagaattgg gtgccgtcat agcagaatag gcattactcg acagagaaga gtaagaaatg 5160 gaactagtag atcctaactt agatccctgg aaccatccag gaagccagcc tacaactcct 5220 tgtaccagat gttattgtaa atggtgttgc tttcattgtt actggtgctt tacaacgaag 5280 ggcttaggca tctcctatgg caggaagaag cggagacagc gaccaagaac tcctcaaagc 5340 agtcagatac atcaagattt tgtaccaaag cagtaagtat tgttaagcat atgtaatgtc 5400 aaatttgtta gcaataggca tagcagcatt aatagtagca ctaataataa caatagttgt 5460 gtggactata gcatatatag aatataagaa actggtaagg caaagaaaaa taaataggtt 5520 atataaaaga ataagcgaaa gagcagaaga cagtggcaat gagagtgagg gggatgcaga 5580 ggaattggca gcacttgggg aagtggggcc ttttattcct ggggacatta ataatctgta 5640 atgctgcaga aaacttatgg gttacagtct attatggggt acctgtgtgg aaagaagcaa 5700 ccactactct attctgtgca tcagatgcta aatcatatga aaaagaggca cataatgtct 5760 gggctacaca tgcttgtgta cccacagatc ccaatccaca agaagtagtt ctggaaaatg 5820 taacagaaag gtttaatatg tgggaaaata acatggtaga acaaatgcat acagatataa 5880 tcagtttatg ggatcaaagc ctaaagccat gtgtgaagtt aaccccactc tgtgttactt 5940 tagattgtag aaacattgcc accaatggca ccaatgacac tattgccatc aatgacactc 6000 tgaaggaaga tccagaggca atacaaaact gttctttcaa tacaaccaca gaaataagag 6060 ataagcagct gaaagtacat gcactttttt ataaacttga tatagtacaa atcaacaagg 6120 atgacaatag aacatacaga ctaataaatt gtgatgcctc aaccattaca caggcttgtc 6180 caaaggtatc ttgggatcca attcccatac attattgtgc tccagctggt tatgcgattc 6240 taaagtgtaa tgagaaaaat ttcacaggga cagggtcatg caagaatgtc agtacagtac 6300 aatgtacaca tggaattaaa ccagtggtat ccactcaatt gttgttaaat ggcagcctag 6360 cagaaggaga gatagtaatc agatctcaaa atatctcaga taatgcaaaa accataatag 6420 tgcaccttaa tgaatctgta cagattaatt gtacaagacc caacaacaat acaagaaaaa 6480 gaatatcttt aggaccagga cgagtatttt atacaacagg agaaataata ggagacatca 6540 gaaaggcaca ttgtaacgtt agtggaacac aatggaggaa cacgttagca aaggtaaagg 6600 caaagttagg gtcttatttc cctaatgcaa caataaaatt taactcatcc tcaggagggg 6660 acctagaaat tacaaggcat aattttaatt gtatgggaga atttttctac tgtaatacag 6720 atgaactgtt taatgacaca aaattcaatg acacaggatt caatggcact atcactctcc 6780 catgtcgaat aaaacaaatt gtaaacatgt ggcaggaagt gggacgagca atgtatgcca 6840 atcccattgc aggaaacatt acctgtaact caaatattac aggtctgcta ttgacaagag 6900 atggtggtct gaatagtact aatgagacct tcagacctgg gggaggaaat atgaaagaca 6960 attggagaag tgaattatat aaatataaag tagtagaaat tgaaccacta ggagtagcac 7020 ccaccaaggc aaaaagacaa gtggtgaaga gagaaagaag agcagtggga ctaggagctc 7080 tgttccttgg gttcttggga gcagctggaa gcactatggg cgcggcgtca ataacgctga 7140 cggtacaggc cagacaatta ttgtctggaa tagtgcaaca gcagagcaat ctgctgaggg 7200 ctattgaagc gcaacagcat ctgttgcagc tcacagtctg gggcattaaa cagctccagg 7260 caagagtcct ggctgtggaa agatacctaa aggatcaaca gctcctaggg ctttggggct 7320 gctctggaaa actcatctgc accactaatg tgccctggaa ctctagttgg agtaataaat 7380 ctcttgagga gatttggggg aacatgacct ggatggagtg ggaaaaagag gttagcaatt 7440 actcaaaaga aatatacagg ttaattgaag actcgcagaa ccagcaggaa aagaatgaac 7500 aagaattatt agcattggac aaatgggcaa gtctgtggaa ttggtttgac ataacacagt 7560 ggctgtggta tataaaaata ttcataatga tagtaggagg cttgataggc ttaagaatag 7620 tttttactgt gctttctata gtaaatagag ttaggaaggg atactcacct ttgtcatttc 7680 agacccatat cccaagcccg agggaacccg acaggcccga aggaatcgaa gaaggaggtg 7740 gagagcaagg caaagacaga tccgtgagat tagtgaccgg attcttagct cttgcctggg 7800 acgacctgcg gaacctgtgc ctcttcagct accgccactt gagagacttc atattaattg 7860 cagcgaggat tgtggacagg gggctgaaga gggggtggga agctctcaaa tatctgggga 7920 atctcacaca gtattggggt caggaactaa agaatagtgc tattagcttg cttaatgcca 7980 cagcaatagc agtagctgag tggacagata gagttataga agctttgcaa agagctggta 8040 gagctattct caacatacct agaagaataa gacagggctt ggaaagggct ttgctataaa 8100 atgggtggca agtggtcaaa aagtagtata gttggatggc ctgctataag ggaaagaatg 8160 aggcgaaccc ctccaacccc tccagcagca gagggggtgg gagcagtgtc tcaagactta 8220 gaaagacggg gggcaattac aagcagcaat actagagcta ataatcctga cttggcctgg 8280 ctggaagcac aagaggaaga cgaagtaggc tttccagtca gacctcaggt acctttaaga 8340 ccaatgacct ataagggagc tgtagatctc agtcactttt taaaagaaaa ggggggactg 8400 gaagggttaa tttactccaa gagaagacaa gagatccttg atctgtgggt ctaccacaca 8460 caaggctact tccctgattg gcagaactac acaccagggc cagggatcag atatccactg 8520 accatggggt ggtgcttcaa gctagtacca gttgacccag aggaggtaga aaaggccaat 8580 gaaggagaga acaactgctt gctacacccc atgagccaac atggaatgga ggatgaagac 8640 aaagaagtac tgaaatggga gtttgacagc cgcttggcac tgagacacat agccagagag 8700 agacatccgg agtactacca agactgagac tgctgacaca gagattgctg acacagaaga 8760 atctaaaggg actttccact ggggactttc cagagggtgg gccagagggc gggactgggg 8820 agtggctcac cctcagatgc tgcatataag cagccgcttt tcgcctgtac tgggtctctc 8880 tagttagacc agatttgagc ccgggagctc tctggctagc tagggaaccc actgcttaag 8940 cctcaataaa gcttgccttg agtgcttt 8968 2 8987 DNA Human immunodeficiency virus type 1 isolate=92NG083; 156.362gag; 1727.4465pol; 4410.4988vif; 4928.5218vpr; 5199.7795tat; 5338.8000rev; 5440.5466vpu; 5593.8142env; 8144.8767nef 2 atgaaagcga aagttaatag ggactcgaaa acgaaagttc cagagaagtt ctctcgacgc 60 aggactcggc ttgctgaagt gcacacagca agaggcgaga gcggcgactg gtgagtacgc 120 cattttttga ctagcggagg gctagaagga gagaggtggg tgcgagagcg tcagtattaa 180 gcgggggaaa attagattct tgggaaaaaa ttcggttaag gccaggggga aggaaaaagt 240 ataaactaaa acatatagta tgggcaagca gggaactggg gagatttgca cttaaccgtg 300 accttttaga aacagcagaa ggttgtgtgc aaataatgaa acagttgcaa ccagctctct 360 agacaggaac agaggagctt agatcattat ttaatacagt agcaaccctc tactgtgtac 420 atcaaaagat agaggtaaaa gacaccaaag aagctccaga ggaagtggaa aaaatacaaa 480 agaacagtca gcaagaaata cagcaggcag caaagaatga aggaaacagt aacccagtca 540 gccaaaatta tcctatagtg cagaatgcac aagggcaaat gatacatcag gccatatcac 600 ctaggacttt gaatgcgtgg gtaaaagtag tagaagaaaa ggccttcagt ccagaagtaa 660 tacccatgtt ttcagcatta tcagagggag ccaccccaca agatttaaat accatgctaa 720 atacagtggg ggggcatcaa gcagctatgc aaatgctaaa ggatactatc aatgatgaag 780 ctgcagagtg ggacaggata catccacagc aggcagggcc tattccacca ggccaaataa 840 gagagcctag tggaagtgat atagcaggaa ctactagtac cctgcaggaa caaataagat 900 ggatgaccag caacccacct atcccagtgg gagaaatcta taaaagatgg ataatcctgg 960 gattaaataa aatagtgaga atgtatagcc ctgtcagcat tttggacata agacaagggc 1020 caaaagaacc ctttagagat tatgtagata ggttctttaa aactttgaga gctgagcaag 1080 ctacacagga agtaaaaggt tggatgacag acaccttgtt ggttcaaaat gcgaacccag 1140 attgtaaaac catcttaaga gcattaggac caggagctac actagaagaa atgatgacag 1200 catgtcaggg agtgggagga cccagccata aagcaagagt tttagctgag gcaatgagcc 1260 aggcatcagg tgcagcagca gcagccataa tgatgcagaa aagcaatttt aagggcccga 1320 gaagaattat taagtgtttc aactgtggca aggaaggaca tctagccaga aattgcaggg 1380 cccctaggaa aaagggctgt tggaaatgtg gaaaggaggg acatcaaatg aaagaatgca 1440 cggaaaggca ggctaatttt ttagggaaaa tttggccttc caacaagggg aggccaggaa 1500 actttctcca gaacaggaca gagccaacag ccccaccagc agagagcttc ggattcggag 1560 aggagatagc cccctccccg aagcaggagc caaaggagaa ggagctatat cccttaactt 1620 ccctcaaatc actctttggc agcgacccct agtcacagta aaaatagggg gacagctaat 1680 agaagcccta ttagacacag gagcagatga cacagtatta gaaggaataa atttaccagg 1740 aaaatggaaa ccaaaaatga tagggggaat tggaggtttt atcaaagtaa gacagtatga 1800 tcaaatactt atagaaattg gtggaaaaaa ggctataggg acagtattag taggacctac 1860 acctattaac ataattggga gaaatatgtt gactcagatt ggttgtactt taaactttcc 1920 aataagtcct attgaaactg taccagtaaa attaaagcca ggaatggatg gcccaagggt 1980 taaacaatgg ccattgacag aagagaaaat aaaagcatta acagaaattt gtaaagacat 2040 ggaaaaggaa ggaaaaattt caaaaattgg gcctgaaaat ccatataaca ctccaatatt 2100 cgccataaag aaaaaagaca gtactaaatg gagaaaattg gtagatttca gagaacttaa 2160 taaaagaact caagacttct gggaggtcca attaggaata cctcaccccg cggggttaaa 2220 aaagaaaaga tcagtaacgg tactagatgt gggagatgca tacttttcag ttcccttaga 2280 taaagacttt agaaagtata ctgcatttac tatacctagt ataaataatg agacaccagg 2340 gattagatat caatacaatg tgcttccaca gggatggaaa ggatcaccag caatatttca 2400 gagtagcatg acaaaaattt tagagccttc tagaacaaaa aatccagaaa tggtgatcta 2460 ccaatacatg gatgatttat atgtaggatc tgacttagaa atagggcagc atagagcaaa 2520 aatagaggag ttaagagaac atctactgaa atggggattg accacaccag ataaaaaaca 2580 tcagaaagaa cctccattcc tttggatggg atatgagctc catcctgaca aatggacggt 2640 acaacctata cagctgccag aaaaggaaga ttggactgtc aatgatatac aaaagttagt 2700 gggaaaacta aattgggcaa gtcagattta tccagggatt aaagtaaagc acctatgtag 2760 actccttagg ggggccaaag cactaacaga catagtaccc ctaacggcag aagcagaaat 2820 ggagctggca gagaacaggg aaattctaaa agaacctgta catggagtct atcatgaccc 2880 atcaaaagaa ttaatagcag aagtacagaa gcaagggcca gaccaatgga catatcaaat 2940 ttatcaagag ccatacaaaa atctaaaaac aggaaaatat gcaaaaaggg ggtctgccca 3000 cactaatgat gtaaaacaat taacagaagt agtgcaaaaa atagccacag agggcatagt 3060 aatctgggga aagattccta aatttaaact acctatacga aaagaaacat gggaagtatg 3120 gtggacagag tactggcagg ccgcctggat tcctgagtgg gagtttgtca atacccctcc 3180 tctagtaaaa ctatggtatc aattagaaac agaacccata ccaggagcag aaacttacta 3240 tgtagatggg gcagctaata gggagacaaa attaggaaag gcaggacatg ttactgacaa 3300 aggaaaacaa aaaattatta ccctaactga aacaacaaac caaaaggctg aattacatgc 3360 aattcaacta gctttgcagg actcaagacc agaagtaaac atagtaacag actcacagta 3420 tgcattagga atcattcaag cacaaccaga taggagtgga tcagaattag tcaatcaaat 3480 aatagaacag ctaataaaaa aggaaaaggt ctacctgtca tgggtaccag cacacaaagg 3540 gattggagga aatgaacaag tagataagct agtcagtagt ggaatcagga aagtattatt 3600 tttggatggc atagataaag cccaagaaga acatgaaaga tatcacagca attggagagc 3660 aatggctagt gattttaatc tgccacctgt agtagcaaaa gaaatagtgg ccagctgtga 3720 taaatgtcaa ctaaaagggg aagccatgca tggacaagta gactgtagtc caggaatatg 3780 gcaattagat tgtacacatt tagaaggaaa aattatcata gtagcagttc atgtagccag 3840 tggctatata gaagcagaag ttatcccagc agaaacaggg caggaaacag catactttat 3900 attaaaatta gcaggaaggt ggccagtaaa agtgatacat acagacaatg gtcccaattt 3960 catcagtgct gcagtaaagg cagcatgttg gtgggcaaat atcacacagg aatttggaat 4020 tccctacaat ccccaaagcc aaggagtagt ggaatctatg aataaggaat taaagaaaat 4080 catcggacag gttggagatc aagctgaaca tcttaagaca gcagtacaga tggcagtatt 4140 cattcacaat tttaaaagaa aaggggggat tggggggtac agtgcagggg aaagaataat 4200 agacataata gcatcagata tacaaactaa agaactacaa aaacaaatta taaaaattca 4260 aaattttcgg gtttattaca gggacagcag agacccaatt tggaaaggac cagcaaagct 4320 actctggaaa ggtgaagggg cagtagtaat acaggacaat aacgaaataa aggtagtacc 4380 aagaagaaaa gcaaagatcc ttaaggatta tggaaaacag atggcaggtg gtgattgtgt 4440 ggcaggtaga caggatgagg attagaacat ggaacagttt agtaaaacat catatgtatg 4500 tctcaaagaa agctaaaggc tggttttata gacatcacta tgaaagcagg catccaagag 4560 taagttcaga agtacacatc ccactaagag atgctacact agtagtaaga acatattggg 4620 gtctgcatgc aggagaaaaa gactggcaat tgggccatgg ggtttccata gaatggaggc 4680 agaaaagata tagtacacaa atagacccta acacagcaga ccatctgatt catctgtatt 4740 attttgactg tttttcagaa tctgccataa gaaaagccat attaggagag atagttagcc 4800 ctaggtgtga atacccagca ggacataata aggtaggatc tctacaatat ctggcatcga 4860 aagcattagt aacaccaaca aggaaaaggc cacctttgcc aagtgttggg aaattagcag 4920 aagatagatg gaacaagccc cagaagacca gggaccacag agagaaccct acaatgaatg 4980 gacattagaa ctgttagaag agcttaaaaa tgaagctgtt agacattttc ctaggccctg 5040 gctccatggc ttaggacagt atatctataa cacttatggg gatacttggg aaggagttga 5100 agccataata agaatactac aacaactact gtttatccat ttcagaatcg ggtgccaaca 5160 tagcagaata ggcattactc cacagagaag agtaagggat ggacccggta gaccctaagc 5220 tagagccctg gaatcatccg gggagtcagc ctacaactcc ctgtaacaaa tgttattgta 5280 aagtgtgctg ctggcattgt caagtttgct ttttaaacaa aggcttaggc atctcctatg 5340 gcaggaagaa gcggagaccc cgacgaggaa ctcctcaggg cagtaaggat catcaaaacc 5400 ctgtaccaaa gcagtaagta gtaacaatta atatatgtaa tgcaggcctt agaaatatct 5460 gactaatagt agcattcata gcagccacaa ttgtgtggag tatagtattt atagaatata 5520 gaaaaataag aaaacagaaa aaaatagaaa agttacttga tagaataaga gaaagagcag 5580 aagacagtgg aaatgagagt gaaggggata cagaggaatt ggcaacactt atggaaatgg 5640 gggactttga tccttgggtt ggtaataatt tgtagtgcct cagataactt gtgggtcaca 5700 gtctattatg gggtacctgt gtgggaagat gcagataccc ccctattctg tgcctctgat 5760 gctaaatcat atagttctga aaaacataat gtctgggcta cacatgcctg tgtacccaca 5820 gaccctaacc cacaagaaat agctatagaa aatgtaacag aaaattttaa catgtggaag 5880 aataacatgg tagaacagat gcaggaggat ataatcagtt tatgggagga aagcctaaag 5940 ccatgtgtaa agctaactcc tctctgtatc actttaaact gtactaatgt aaacagtgct 6000 aatcatactg aggccaataa cactgtagaa aacaaagaag aaataaaaaa ctgctctttc 6060 aagataacca cagaaagggg aggcaagaag aaggaagaat acgcgctttt ctataaactt 6120 gatgtggtac caattagtaa tgggaataag actagttata ggctaataca ttgtaatgtc 6180 tcaaccatta aacaggcttg tccaaaggta aattttgacc caattcccat acattattgt 6240 gctccagctg gttttgcgat tttaaagtgt agggataagg agtacaatgg aacaggacca 6300 tgtaaaaatg tcagtacagt acaatgtaca catggaatta agccagtggt atcaactcaa 6360 ctactgctga atggcagttt agcagaagaa gatataagaa ttagatctga aaatttcaca 6420 gacaatacca aagtcataat agtgcagctt aataatagta tagaaattaa ttgtatcaga 6480 cccaataaca atacaagaaa aagtatacca atcggaccag gacaagcgtt ctatgcaaca 6540 ggtgatataa taggagacat aagacaagca cattgtaatg ttagtagaat aaaatggagg 6600 gagatgttaa agaatgtcac agcacagcta aggaaaatct ataataataa gaacataacc 6660 tttaactcat ctgcaggagg ggacctagaa attacaacac atagtttcaa ttgtagagga 6720 gagtttttct attgcaatac atcaggactg tttaataata atattagtaa tattaataat 6780 gagactatca cactcccatg taaaataaaa caaattgtga ggatgtggca gaaagtggga 6840 caagcaatgt atgcccttcc catcgcagga aaccttgtat gtaaatcaaa cattacagga 6900 ttaatattaa caagagatgg tgggaataac aatgacagta cagaggagac cttcagacct 6960 ggaggaggag atatgaggga caattggaga agtgaattat ataagtataa aacagtaaaa 7020 atcaaatcac taggagtagc acccaccagg gcaaggagaa gagtggtgga gagagaaaaa 7080 agagcagttg gactgggagc tgtcttcctt gggttcttag gagcagcagg gagcactatg 7140 ggcgcggcgt caataacgct gacggcacag gtcagacaat tattgtctgg catagtgcaa 7200 cagcaaagca atttgctgag ggctatagag gcgcagcagc atctgttgca actcacagtc 7260 tggggcatta aacagctcca gtcaagagtc ctggctatag aaagatacct aaaggatcaa 7320 cagctcctag ggatttgggg ctgctctgga aaactcatct gcaccactaa tgtgccctgg 7380 aacactagtt ggagtaataa atcttataat gagatttggg ataacatgac ttggctagaa 7440 tgggaaaggg aaattcacaa ttacacacaa cacatataca gcctgattga agaatcgcag 7500 aaccagcagg aaaagaatga acaagactta ttggcattgg acaagtgggc aagtttgtgg 7560 aattggtttg acatatcaaa ttggctatgg tatataagaa tattcataat gatagtagga 7620 ggtttaatag gtttaagaat agtttttgct gtgctttcta tagtaaatag agttaggcag 7680 ggatactcac ctttgtcgtt ccagaccctt acccatcacc agcgggaacc cgacaggctc 7740 ggaaaaaccg aagaaggagg tggcgagcaa gacagagaca gatccactcg attagtgagc 7800 ggattcttag cgcttgcctg ggacgacctg cggagcctgt gccttttcag ctaccaccgc 7860 ttgagggact tagtcttgat tgcagcaagg acggtggaac ttctgggacg cagcagcctc 7920 aagggactga gactggggtg ggaaggcctc aagtacttgt ggaacctcct gttgtattgg 7980 ggtcgggaac taaagaatag tgctattaat ttgcttgata caatagcaat agcaacagct 8040 aacgggacag atagggttat agaagtagca caaagagctt atagagctat tctcaacgta 8100 cctacaagga taagacaagg cttagaaaga gctttgctat aaaatggggg gcaagtggtc 8160 aaaaagtagc atagttggat ggcctcagat aagggaaaga ataagacaaa ctcctgtagc 8220 agcagaagga gtaggagcag tatctcaaga tttagctagg catggagcaa tcacaagcag 8280 caatacagca accaacaatc ctgattgtgc ctggctggaa gcacaagagg aggactcaga 8340 tgtaggcttt ccggtcagac cacaggtacc tttgagacca atgacttata aggctgcttt 8400 tgatctcagc ttctttttaa aagaaaaggg gggactggat gggctaattt actccaagag 8460 aagacaagac atccttgatc tatgggtcta taatacacaa ggattcttcc cagattggca 8520 gaactacaca ccagggccag ggactagact cccactgacc tttgggtggt gcttcaaact 8580 agtaccaatg gacccagcag agatagagga agccaataag ggagagaaca tcagtctatt 8640 acaccccatc tgccagcatg gaatggagga tgaagacaga gaagtgctgg tatggagatt 8700 taacagtagc ctagcacgga gacacctagc ccgagagctg catccggagt actacaaaga 8760 ctgctgacac agaagttgct gacaagggac tttccgcctg ggactttcca ggagaggcgc 8820 ggcctgggag gggctgggga gtggctaacc ctcagaagct gcatataagc agccgcttct 8880 cgcctgtact gggtctctct tgttggacca gatttgagcc tgggagctct ctggttggca 8940 ggggaaccca ctgcttaagc ctcaataaag cttgccttga gtgcttc 8987 3 8953 DNA Human immunodeficiency virus type 1 isolate=“90CR056”; 137..1639gene=“gag”; 4388..4966gene“vif”; 4906..5196gene “vpr”; 5177..7782gene=“tat”; 5316..7972gene=“rev”; 5408..5650gene=“vpu”; 5577..8114gene=“env”; 8117..8737gene=“nef” 3 ttgatagtga aagtaaaacc agagaagatc tctcgacgca ggactcggct tgctgaagtg 60 cacacagcaa gaggcgagag cggcgactgg tgagtacgcc attttgtttt gactagcgga 120 ggctagaagg agagagatgg gtgcgagagc gtcagtatta agcggcggaa aattagatgc 180 ttgggagaaa attcggctaa ggccaggggg aaagaaaaaa tataggctaa aacatctagt 240 atgggcaagc agggagctgg aaagatttgc acttaacccc ggccttttag aaacaccaga 300 aggctgtcta cagataatag aacagataca gccagctatt aagacaggaa cagaagaact 360 taaatcatta tttaatctag tagcagtcct ctattgcgta catcgaaaaa tagatgtgaa 420 agacaccaag gaggctttag ataagataga ggaaatacaa aacaaaagtc agcaaaaaac 480 acagcaagca gcagctgata aggaaaaaga caacaaggtc agtcaaaatt atcctatagt 540 acagaatgct caagggcaga tggtacacca ggccatatca cctaggacct taaatgcatg 600 ggtaaaagta gtagaagaaa aggcttttag cccagaagta atacccatgt tttcagcatt 660 atcagaagga gccaccccac aagacttaaa tgctatgcta aatacagtgg ggggacatca 720 agcagccatg cagatgttaa aagatacaat caatgaggaa gctgcagaat gggacagggt 780 acatccagtg catgcagggc ctattccacc aggccaaatg agagaaccaa ggggaagcga 840 tatagcagga actactagta ccctgcagga acaaatagca tggatgacag gcaatccagc 900 tatcccagtg ggagacatct ataaaagatg gataatcctg ggattaaata agatagtaag 960 aatgtatagt cctgtcagca ttctggacat aaaacaaggg ccaaaagaac cctttagaga 1020 ctatgtagac aggtttttta aaactttaag agctgagcaa gccacacagg atgtgaagaa 1080 ttggatgaca gaaaccttgt tggtccaaaa tgcaaatcca gattgcaaga ctatattaag 1140 agcattagga caaggggctt caatagaaga aatgatgaca gcatgtcagg gagtgggagg 1200 acctagtcat aaagcaagag ttttggctga ggcaatgagc caagtaacaa atacaaatac 1260 agccataatg atgcagaaag gcaactttaa gggccaaaga aaatttgtta aatgcttcaa 1320 ctgtggcaaa gagggacaca tagccagaaa ttgcagggcc cctaggaaaa agggctgttg 1380 gaaatgtgga agagaaggac atcagatgaa agactgcaca gagagacagg ctaatttttt 1440 agggaaaatt tggccttcca gcaaagggag gccaggaaat tttctccaga gcaggccaga 1500 accaacagcc ccaccagcag agagcttcgg gttcggagag gagatgaccc cctctccgaa 1560 gcaggagcag ctgaaggaca aggaacctcc cttagcttcc ctcagatcac tctttggcag 1620 cgaccccttg ttacagtaaa aatagaggga cagttaaggg aagctctatt agatacagga 1680 gcagatgata cagtattaga agagataaat ttgccgggaa aatggaaacc aaaaatgata 1740 gggggaattg gaggttttat caaagtaaga cagtatgagc aagtagccat agaaatctgt 1800 ggaaaaaagg ctataggtac agtattagta ggacctacac ctgtcaatat aattggaagg 1860 aatatattga ctcaaattgg ttgcacctta aattttccaa ttagtcctat tgaaactgta 1920 ccagtaaaat taaagccagg aatggatggc ccaaaggtta aacaatggcc attgacagaa 1980 gaaaaaataa aagcattaac ggaaatttgt acagagatgg aaaaagaagg aaaaatctca 2040 agaatagggc ctgagaatcc atacagcact ccaatatttg ccataaaaaa gaaggatagt 2100 actaaatgga gaaaattagt ggatttcaga gaactcaata aaagaactca agacttctgg 2160 gaagttcagt taggaatacc acacccagca gggttaaaaa agaaaaaatc agtatcagta 2220 ctggatgtgg gggatgcata tttttcagtc cctttagata aagaattcag aaagtatact 2280 gcattcacca tacctagtat aaacaatgag acaccaggga ttagatatca gtataatgtg 2340 cttccacagg gatggaaagg atcaccagca atattccaga gtagcatgac aaaaatctta 2400 gcgcccttta gagaacaaaa tcctgaaatg gttatttacc aatacatgga tgatttgtat 2460 gtaggatctg acttagaaat agggcaacat agagcaaaaa tagaggagtt aagagctcat 2520 ttgttgaaat ggggatttac cacaccagac aaaaaacatc agaaagaacc cccatttctt 2580 tggatgggat atgaactcca tcctgacaaa tggacagtac agactgtaaa actgccagaa 2640 aaagacagct ggactgtcaa tgatatacag aagttagtgg gaaaactaaa ttgggcaagt 2700 cagatttatc caaatattaa agtaaagcaa ctatgtaaac tccttagggg ggccaaagca 2760 ttaacagaca taataccact gacaaaagag gcagaattgg aattggcaga aaacagggag 2820 attctgagag aaccaataca tggagtatat tatgatccat caaaagactt aatagcagaa 2880 atacggaagc aagggcaagg ccaatggaca tatcaaattt atcaggagcc atttaaaaat 2940 ctgaagacag gaaaatatgc aaaaatgaga actgcccaca ctaatgatat aaaacaatta 3000 acagaagcag tgcaaaagat atctacagaa agcatagtaa tatggggaaa aattcctaaa 3060 tttagactac ctatacaaaa agaaacatgg gagacctggt ggacagagta ttggcaagcc 3120 acatggattc ctgaatggga gtttgttaac acccctcatc tagtaaaatt atggtatcag 3180 ttagaaacag agcccatagc aggagcagaa acttactata tagatggggc agctaatagg 3240 gaaactaaat taggaaaagc aggatatgtc actgatagag gaaagcaaaa agttgtctcc 3300 ctaacggaaa caacaaatca gaagactgaa ttacaagcaa tttatctagc tttgcaagat 3360 tcagggttag aagtgaacat agtgacagat tcacagtatg cactaggaat cattcaagca 3420 caacccgata agagtgaatc agagttagtt aatcaaataa tagaggaatt aataaagaag 3480 gaaaaggtct acctgtcatg ggtaccagca cacaaaggaa ttggaggaaa tgaacaagta 3540 gataaattag ttagttctgg agtcagaaaa gtgctatttc tagatgggat agataaagct 3600 caagaagaac atgaaaggta tcataacaat tggagagcag tggctagtga ttttaatcta 3660 ccacctatag tagcaaaaga aatagtagct agctgtgata aatgtcagct aaaaggggaa 3720 gccatgcatg gacaagtaga ctgtagccca ggaatatggc aattagattg cacacatttg 3780 gaaggacaag ttattctggt agcagtccat gtagccagtg gctatataga agcagaagtc 3840 atcccagcag aaacaggaaa ggaaacagca tacttcctgt tgaaactagc aagcagatgg 3900 ccagtaaaag taatacatac agacaatggc agcaatttca cgagtgctgc ggttaaggca 3960 gcctgttggt gggcagatat ccaacaggaa tttgggattc cctacaatcc ccaaagtcag 4020 ggagtagtag aatctatgaa taaagaatta aagaagatca tagggcaggt aagagaccaa 4080 gcagaacacc ttaagacagc agtacaaatg gcagtattca ttcacaattt taaaagaaaa 4140 ggggggattg gggggtacag tgcaggggaa agaataatag acataatagc aacagacata 4200 caaactaaag aattacaaaa acaaatttca aacattcaaa aatttcgggt ttattacagg 4260 gacagcagag acccaatttg gaaaggacca gcaaaactcc tctggaaagg tgaaggggca 4320 gtagtaatac aagacaatag tgaaataaaa gtagtaccaa gaagagaggc aaaaatcatt 4380 agggattatg gaaaacagat ggcaggtgat gattgtgtgg caagtagaca ggatgaggat 4440 taacacatgg aaaagcttag taaagtacca tatgcatatt tcaaggaaag ctagaggatg 4500 gttttataga catcattttg aaagcactca tccaaggata agttcagaag tacacatccc 4560 attaggagaa gctaggttag tcataaccac atactggggt ctgaatacag gagaaagaga 4620 atggcattta ggccagggag tctccataga atggagactg aaaaggtata gcacacaagt 4680 agagcctggc ctggcagacc aactaattca tatgcattat tttgattgtt tttcagaatc 4740 tgccataagg aaagccatat taggacgtgt agttagacct aggtgtaact atccagcagg 4800 acataaacag gtaggaactc tacaatactt ggcattaaca gcattagtgg caccaaaaaa 4860 gataaagcca cctttgccta gtgttagaaa gctagtagag gatagatgga acaagcccca 4920 gaagaccagg ggccacagag ggagccacac aatgaatgga cactagagct tttagaggag 4980 attaagaatg aggctgttag gcattttcct agagtatggc tccatcaatt aggacagcat 5040 atctataaca cctatggaga tacttgggta ggagttgaag ctttaataag aacgctgcaa 5100 caactactgt ttattcattt cagaattggg tgccaacata gcagaatagg aattactcga 5160 cagagaagag taagaaatgg acccagtaga tcctaaacta gagccctgga accatccagg 5220 aagtcagcct caaactgctt gtaacaattg ttattgtaaa aagtgctgct atcattgcca 5280 aatgtgcttt ttaaagaaag gcttaggaat ttcctatggc aggaagaagc ggagccagcg 5340 acacagaact cctgcaagtt tgcaagatca tcaaaattct atatcaaagc agtaagtatt 5400 atcataaatg tatatattag gattaggaat aggagcgcta gtagtaacat ttatcatagc 5460 cgtaattgtg tggaccatag tatatataga atataaaaaa ttggtaaggc aaaagaaaat 5520 agacaggcta attgaaagaa taggagaaag agcagaagac agtggcaacg agagtgatgg 5580 agacacagag gaattatcca agcttatgga gatggggcac cttaatcttg ggtatgttgc 5640 tgatctgtag tgctgcacaa aacttgtggg ttacagtata ttatggggta cctgtgtgga 5700 aagaggcaaa aaccactcta ttctgtgcat cagatgctaa ggcatatgag acagaaaagc 5760 ataatgtctg ggctacacat gcatgtgtac ccacagaccc caacccacaa gagatggtca 5820 tggagaatgt aacagagagc tttaatatgt gggaaaataa catggtggag cagatgcata 5880 cagacataat cagtttatgg gatcaaagct tgaaaccatg tgtaaaatta accccactct 5940 gtgttactct aaactgtact aatgtcagaa acaatacctc taacagcact agcagtatgg 6000 aggcaggagg ggaactaaca aattgctctt tcaatgtaac tacagtacta agagataagc 6060 agcagaaagt acatgcactc ttttatagac ttgatgtagt accaattgat aacaatagta 6120 ctcagtatag gctaataaat tgtaatacct cagtcattac acaggcttgc ccaaaggtgt 6180 cctttgaacc tattcccata cattattgtg ctccagctgg ctttgcgatt ctaaagtgta 6240 acaataaaac attcaatgga acaggattat gtacaaatgt cagtacagta caatgtacac 6300 atggaattag accagtggta tcaactcaac tgctattaaa tggaagccta gcagaagaac 6360 agatcataat tagaactaaa aatatctcag acaataccaa aaacataata gtacagctta 6420 agacaccagt aaacattaca tgtaccaggc ctaacaataa tacgagaaca agtatacatt 6480 tagggccagg acgagcattc tatgcaacag gtgacatcat aggagatata agacaagcac 6540 attgtaatat tagtagaaca gactggaata agactttaca ccaggtagtt acacaattag 6600 gaatacactt gaacaataga acaataagct ttaagccaaa ctcaggaggg gacatggaag 6660 ttagaacaca tagttttaat tgtagaggag aatttttcta ttgcaataca tcagggctgt 6720 ttaatagtag ttgggaaatg catactaatt acacatcaaa tgacacaaag ggaaacgaaa 6780 acattacact gccatgcaga ataaaacaaa ttgtaaacat gtggcagaga gtaggacgag 6840 caatgtatgc ccctcccatc caaggaaaca ttatgtgtgt atcaaatatt acaggactaa 6900 tattgacaat tgacgagggt aacgcgtctg cagaaaatta taccttcaga cctggaggag 6960 gagatatgag ggacaattgg agaagtgaat tgtataaata taaagtagta aaaattgaac 7020 cactgggaat agcacccacc aagacaagga gaagagtggt ggagagagaa aaaagagcag 7080 tgggaatggg agcttctttc cttgggttct tgggagcagc aggaagcact atgggcgcgg 7140 cgtcaataac gctgacggta caggccaggc aattattgtc tggtatagtg cagcagcaaa 7200 gcaatttgct gagagctata caggcgcgac agcatatgtt gcagctcacg gtctggggca 7260 ttaaacagct ccaggcaaga gtcctcgctg tggaaagata cctaagggat caacagctcc 7320 tggggatttg gggctgctct ggaaaactca tctgcaccac taatgtgcct tggaactcta 7380 gttggagtaa taaatcacag agtgaaatct gggacaacat gacttggatg gaatgggata 7440 aacaaattag caattacaca gaggaaatat acaggttgct tgaagtctcg caaacccagc 7500 aggaaaagaa tgaacaggac ttattagcat tggacaaatg ggcaagtctg tggacttggt 7560 ttgacatatc acattggctg tggtatataa aaatattcat aatgatagta ggaggtttaa 7620 taggtttaag aataattttt gctgtgcttt ctatagtaaa tagagttagg cagggatact 7680 cacctttgtc ttttcagacc cttgtcccga acccacgggg acccgacagg cccgaaggaa 7740 cagaagaagg aggtggcgag caagacagag acagatccgt gagattagtg aacggattct 7800 taccagttgt ctgggacgac ctccggagcc tgtcactctt cagctaccgc ctcttgagag 7860 acttactctt aattgtagtg aggactgtgg aacttctggg gagaaggggg agggaagccc 7920 tcaaatatct ctggaatctt ctacaatact ggggacagga actaaagaat agtgctattg 7980 atttgcttaa caccacagca atagcagtag ctgagggaac agatgggatt atagtaatag 8040 tgcaaagagc ttggagagct attctccaca tacctagaag aataagacag ggctttgaaa 8100 gaagcttgct ataataatgg gaggcaaatg gtcaaaaagt aggatgggtg ggtggtctac 8160 tataagggaa agaatgaggc gagctgaacc agtagcagaa ggggtaggag cagtgtctcg 8220 agatttggat agacgcgggg cagtcacaat taataataca gcatctacta atcgtgatgc 8280 cgcctggctg gaagcacaag aggacgggga ggaagtaggc tttccagtca ggcctcaggt 8340 acctttaaga ccaatgacct ataagggagc ttttgatctc agccattttt taaaagaaaa 8400 ggggggactg gatgggttaa tttactccaa gcaaagacag gacatccttg atttatgggt 8460 ctataacaca caaggctact tccctgactg gcagaactac acaccagggc caggggagag 8520 atttcccctg acctttgggt ggtgcttcaa gctagtacca gtaaatccac aggaggtaga 8580 acaggccaat gaaggagaga acaacagctt gctacacccc atgagcctgc atggaatgga 8640 ggatgacggg agagaagtgc tgatgtggaa atttgacagt cgactagcat tgacacactt 8700 ggcccgagta aagcatccgg agtacaaaga ctgctgacac agaagatctg aaagggactt 8760 tccgctggga ctttccgggg aggcgtgatc tgggcgggga tggggagtgg ccaaccctca 8820 gatgctgcat ataagcagct gcttttcgct tgtactgggt ctctttggtt agaccagatc 8880 tgagcctggg agctctctgg ctagctaagg aacccactgc ttaagcctca ataaagcttg 8940 ccttgagtgc ttt 8953 4 8992 DNA Human immunodeficiency virus type 1 isolate=92RW009; 139.1624gag; 1690.4428 pol(N-terminus uncertain); 4373.4951vif; 4891.5181vpr; 5162.7801tat; 5301.7958rev; 5403.5648vpu; 5566.8148env; 8150.8773nef 4 atgaaagcga aagtaagacc agaggagatc tctcgacgcg ggactcggct tgctgaaagt 60 gcactcggca agaggcgaga gcggcggctg gtgagtacgc caaattttat ttgactagcg 120 gaggctagaa ggagagagat gggtgcgaga gcgtcaatat taagaggcgg aaaattagat 180 gcctgggaaa aaattaagtt aaagccaggg gggaaagaaa acatatatga tgaaacacct 240 agtatgggca agcagggagc tggaaagatt tgcacttaac cctgaccttt tagagacacc 300 agaaggctgt aaacaaataa tgagacagct gcaaccagct cttcagacag gaacagatga 360 acttaggtca ttatataata cagtagcaac cctctattgt gtacatcaaa agatagatgt 420 aaaagacacc aaggaggcct tagacaagat agaggaagaa caaaacaaaa gtcagcaaaa 480 aacacagcag gcagaagcag ctgacaaagg aaaagtcagt caaaattacc ctatagtgca 540 aaatgcacaa gggcaaatgg tacaccaggc catatcacct agaactttga atgcgtgggt 600 aaaagtaata gaggagaagg cttttagcca agaggtaata cccatgttta cagcattatc 660 agaaggagcc accccacaag atttaaacac catgctaaat acagtggggg gacatcaagc 720 agccatgcaa atgctaaaag atacaatcaa tgaggaggct gcagagtggg atagggtaca 780 tccagtgcag gcagggcctg ttgcgccagg ccagataaga gaaccaaggg gaagtgacat 840 agcaggaact actagtaccc ttcaggaaca aatagcatgg atgacaaata acccacctat 900 tccagtggga gaaatttata aaagatggat aattctgggg ttaaataaaa tagtaagaat 960 gtatagccct gtcagcatat tggacataaa acaagggcca aaggaacctt ttagagacta 1020 tgtagaccgg ttctttaaaa ccttaagagc cgaacaagct tcacaagatg taaaaaattg 1080 gatgacagat accttgttag tccaaaatgc gaacccagat tgtaagacca ttttaagagc 1140 attagggcca ggggcttcat tagaagaaat gatgacagca tgccagggag tgggaggacc 1200 cggccataaa gcaagggttt tggctgaagc aatgagccaa gtacaacaac caaacataat 1260 gatgcagaga ggcaatttta agggccagag aagaattatt aagtgtttca actgtggcaa 1320 agaaggacac ctagccagaa attgcagggc ccctagaaaa aagggctgtt ggaaatgtgg 1380 aaaggaggga caccaaatga aagactgcac tgagagacag gctaattttt tagggaaaat 1440 ttggccttcc aacaagggga ggccaggaaa ttttccccag agcagactgg agccaacagc 1500 cccaccagca gagaactttg gaatggggga agagatagcc tctcctctga aacaggagca 1560 gaaagacagg gaacctttaa tttccctcaa atcactcttt ggcaacgacc ccttgtcaca 1620 gtaaaaatag gaggtcagct aagagaagct ctattagata caggagcaga tgatacagta 1680 ttagaagaaa taaatttgcc aggaaaatgg aaaccaaaaa tgataggggg aattggaggt 1740 tttatcaagg taaaacagta tgatcaaata cttatagaaa tttgtggaaa aaaggctata 1800 ggtacagtat tagtaggacc tacatctgtc aacataattg gaagaaatat gttgacccag 1860 attggttgta ctttaaactt tccaattagt cctattgaga ctgtaccagt agcattaaag 1920 ccaggaatgg atggcccaaa ggttaaacaa tggccattga cagaagaaaa aataaaagca 1980 ttaagagaaa tttgtacaga aatggaaaaa gagggaaaaa tttcaaaaat cgggcctgaa 2040 aatccatata acactccagt atttgccata aaaaagaagg acagtactaa gtggagaaaa 2100 ttagtagatt tcagggaact caacaaaaga actcaagact tttgggaagt ccaattaggg 2160 ataccacacc cagcagggtt aaagaagaaa aaatcagtga cagtactgga tgtgggggat 2220 gcatacttct cagttccttt agatgagagc ttcaggaaat atactgcatt caccatacct 2280 agtataaaca atgaaacacc aggaattagg tatcaatata atgtgcttcc acagggatgg 2340 aaaggatcac cagcaatatt ccaaaatagt atgacaaaaa tcttagagcc ctttagggca 2400 caaaaccaag aaatagtgat ctatcaatat atggatgact tgtacgtagg atctgactta 2460 gaaatagggc aacatagagc aaaaatagag gagttaagag aacatctatt aaagtgggga 2520 tttaccacac cagacaagaa acatcagaaa gaacctccat ttctttggat ggggtatgaa 2580 cttcatcctg acaaatggac agtacaacct atacagctgc cagaaaagga tagctggact 2640 gtcaatgata tacagaagtt agtgggaaaa ttaaactggg caagtcagat ttacccaggg 2700 gttaaagtaa ggcaattgtg taaactcctt aggggaacca aagcattaac agacatagta 2760 ccactaactg aagaagcaga attagaattg gcagaaaaca gggaaatttt aaaagaacca 2820 gtacatggag tatattatga cccatcaaaa gacttaatag ctgaaataca gaaacagggg 2880 catgaccaat ggacatatca aatttaccaa gaaccattca aaaatctgaa aacaggaaag 2940 tatgcaaaaa ggaggactgc ccacactaat gacgtaaaac agttaacaga ggcagtgcaa 3000 aagatagcca tggaaagcat agtaatatgg ggaaagactc ctaaatttag attacccatc 3060 cagaaagaaa catgggaaac atggtggaca gactattggc aagccacctg gattcctgag 3120 tgggagtttg ttaatacccc tcccctagta aaattatggt accagctaga gaaagaaccc 3180 atattaggag cagagacttt ctatgtagat ggagcagcta atcgggaaac taaaatagga 3240 aaagcagggt atgttactga cagaggaagg cagaaaattg tttctctaac tgaaacaaca 3300 aatcagaaga ctgaattaca agcaattcag ctagctttac aggattcagg atcagaagta 3360 aacatagtaa cagactcaca gtatgcatta ggaatcattc aagcacaacc agatagcagc 3420 gaatcggagg cagtcaatca aataatagaa cagttaataa aaaaggaaag agtctacctg 3480 tcatgggtac cagcacataa aggaattgga ggaaatgaac aagtagataa attagtaagt 3540 agtggaatca ggagagtgct gtttctagat ggaatagata aggctcaaga agaacatgaa 3600 agatatcaca gcaattggag agcaatggct agtgatttta atctgccacc tatagtagca 3660 aaggaaatag tagccagctg tgataagtgt cagctaaaag gggaagccat gcatgggcaa 3720 gtagactgta gtccagggat atggcaatta gactgtacac atctggaagg aaaaataatc 3780 ctggtagcag tccatgcagc cagtggttat atagaagcag aggttattcc agcagaaaca 3840 ggacaagaaa cagcatactt tatactaaaa ttagcaggaa gatggccagt caaagtaata 3900 catacagaca atggcagtaa tttcaccagt aatacagtta aagcagcctg ttggtgggca 3960 ggtatccaac aggaatttgg aattccctac aatccccaaa gtcagggagt aatagaatcc 4020 atgaataaag aattaaagaa aatcataggg caggtaagag atcaagctga gcaccttagg 4080 acagcagtac aaatggcagt attcattcac aattttaaaa gaaaaggggg gattgggggg 4140 tacagtgcag gggaaagaat aatagacata atagcaacag acatacaaac taaggaatta 4200 caaaaacaaa ttacaaaaat tcaaaatttt cgggtttatt acagggacag cagagatcca 4260 atttggaaag gaccagccaa actactctgg aaaggtgaag gggcagtagt aatacaggac 4320 aatagtgata taaaagtagt accaagaaga aaagcaaaga tcattaggga ttatggaaaa 4380 cagatggcag gtgatgattg tgtggcaggt agacaggatg aagattagaa catggaatag 4440 tctagtaaag caccatatgt atgcttcaag gagagctaag ggatggtttt atagacatca 4500 ttatgaaagc agacatccaa aaataagttc agaagtacac atcccattag gggaagctag 4560 attagtaata aaaacatatt ggggtttgca aacaggggaa agagattggc atttgggtca 4620 tggagtctcc atagaatgga gattgagaag atataagaca caagtagacc ctggcctggc 4680 aggccaacta atccatatgc attattttga ttgttttgca gactctgcca taaggaaagc 4740 catattagga catatagtta gccctaggtg tgactatcaa gcaggacata ataaggtagg 4800 atctctacaa tacttggcac tgacagcatt gataaaacca aaaaagataa agccacctct 4860 gcctagtgtt agtaaattag tagaggataa atggaacaag ccccagaaga ccaggggccg 4920 cagagggaac catacaatga atggacacta gagcttttag aggcactcaa gcaggaagct 4980 gtcagacact ttcctagacc atggctccat gacttaggac aatatatcta tgaaacctat 5040 ggggatactt ggaggggagt agaagctata ataagaattc tgcaacaact actgtttatc 5100 catttcagaa ttgggtgccg gcatagcaga ataggcattt tgcaacagag aagagcaaga 5160 aatggagcca gtagatccta aactagagcc ctggaaccat ccaggaagtc agcctaaaac 5220 tgcctgtaat aactgttatt gtaaacactg tagctatcat tgtctagttt gcttccaggc 5280 aaaaggctta ggcatttcct atggcaggaa gaagcggaga cagcgacgaa acgctcctcc 5340 aagcagtgaa gatcatcaaa atcctatatc aaagcagtaa gtagtaataa acagtatatg 5400 taatgacttc tttagaaatc tatgcaatag tagcactgat agtggcgcta atcatagtga 5460 tagttgtgtg gactttagca ggtatagaat ataagaaatt gctaaagcaa aggaaaatag 5520 ataggttaat taagaaaata agagaaagag cagaagatag tggcaatgag agtgatgggg 5580 acattgatga attatcaaaa cttgtggggg tggggaacta tgatcttggg gatgttaaca 5640 atttgtagtg ctgcaaacaa cttgtgggtt actgtctact atggggtacc tgtgtggaaa 5700 gacgcagaga ccaccttatt ttgtgcatca gatgctaaag catatgatcc agaaaagcat 5760 aatgtctggg ctacacatgc ctgtgtaccc atagaccccg acccacaaga aatacatttg 5820 gaaaatgtga cagaagagtt taacatgtgg aaaaataaca tggtagagca gatgcataca 5880 gatataatca gtctatggga ccaaagccta aagccatgtg taaagttaac ccctctctgc 5940 gttactttag agtgtaacaa catcaccaat gtcaacaaca ctgtcaacat tacggatgac 6000 atgaaaggag aaataaaaaa ctgctctttc aatatgacca cagaattaag ggataagaaa 6060 cagagagtgt attcactttt ttataggctt gatatagtac aaattaatag caatagtaat 6120 aacagtagtc ataatcagta taggttaata aattgtaata cctcagccat tacacaggct 6180 tgtccaaagg tatcctttga gccaattccc ataaattatt gtgccccagc tggtttcgcg 6240 attctaaagt gtaaagataa aaagttcaat ggaacagggc catgcaagaa tgtcagcaca 6300 gtacaatgca cacatggaat caagccagta gtatcaactc agctgctgtt aaatggcagt 6360 ctagcagaag aagagataat aattagatct gaaaatatta caaacaatgc caaaaccata 6420 atagtacaac ttaacgagac tgtacaaatt aattgttcca gacctaacaa caatacaaga 6480 aaaagtgtac atataggacc aggacaagca ttttatgcaa caggtgacgt aataggggat 6540 ataagacaag catattgtac tgtcaatgga acaaaatgga atagaacttt acaaaaggta 6600 gcagaaaaat taagtcacta ctttgagaac attacaacaa taatttttaa gaactcctca 6660 gggggggatt tagaaattac aacacatagt tttaattgtg gaggagaatt tttctattgt 6720 aatacatcag gcttgtttaa tagcacctgg agtaaaagaa atggcacctg gcagtcaaat 6780 ggcacagaat taaatataac actcccatgc agaataaagc aaattataaa tatgtggcag 6840 aggacaggac aagcaatgta tgcccctccc atccaaggag taataagctg tgtatcaaac 6900 attacaggac tactattaac aagagatggt ggaaataata atactacaac tgaaaccttc 6960 agacctggag gaggagatat gagggataat tggagaagtg aactatataa atataaagta 7020 gtaaaaattg aaccactagg agtagcaccc accagggcaa agaggagagt ggtggagaga 7080 gaaaaaagag cagttggact gggagctgtc ttcattgggt tcttaggagc agcaggaagc 7140 actatgggcg cggcgtcaat aacgctgacg gtacaggcca gacaattatt gtctggcata 7200 gtgcaacagc aaagcaattt gctgagggct atagaggctc aacagcatct attaaaactc 7260 acagtctggg gcattaaaca gctccaggca agagtcctgg ctctggaaag atacctaagg 7320 gatcaacagc tcctaggaat ttggggctgc tctggaaaac tcatctgcac cactaatgtg 7380 ccctggaact ctagttggag taataagact cagcaggaaa tatgggataa catgacctgg 7440 cagcaatggg ataaagaaat tggcaattac acacaaataa tatatagtct aattgaagaa 7500 tcgcagaacc agcaggaaaa gaatgaacaa gacttattgg cattggacaa gtgggcaaat 7560 ctgtggaatt ggtttgacat atcaaattgg ctgtggtata taaaaatatt cataatgata 7620 gtaggaggct taataggttt aagaataatt tttgctgtgc tctctatagt gaacagagtt 7680 aggcagggat actcaccatt atcgtttcag acccttatcc caaacccgag gggacccgac 7740 aggctcggag gaatcgaaga agaaggtgga gagcaagaca gaggcagatc cattcgatta 7800 gtgagcggat tcttagcact tgcctgggac gacctacgga gcctgtgcct tttcagctac 7860 caccgattga gagacttact attgattgca gcgaggacgg tggaacttct gggacgcagc 7920 agtctcaggg gactacagag ggggtgggaa acccttaagt atctaggaaa tcttgtgcag 7980 tattggggtc tggaactaaa aaggagtgct attaatctgc ttgataccac agcaatagta 8040 gtagctgaag gaacagatag gattatagaa ttaatacaaa gaattagcag agctatctat 8100 aacataccta gcagaataag acagggcttt gaagcagctt tgcaataaaa tgggaagcaa 8160 gtggtcaaaa tgtagtccag taggatggcc tgctgtaaga gaaagactaa ggcaaactga 8220 gccagcagca gagggagtag gagcagcgtc tcaagaccta gacaaatatg gggcacttac 8280 aagtagcaac acacccagca acaatgctga ttgtgcctgg ctggcagcac aagaggagga 8340 aaacgaagta ggctttccag tcagacctca ggtgccttta agaccaatga cttataaagc 8400 agcagttgat ctcagcttct ttttaaaaga aaagggggga ctggaagggt taatttactc 8460 taagaaaagg caagacatcc tggatttgtg ggtctataac acacaaggct acttccctga 8520 ttggcaaaac tacacaccag gaccaggggt cagatatcca ctgacttttg gatggtgtta 8580 caagctagtg ccagttgacc caagggaagt ggaagaagcc aatgaaggag aggacaactg 8640 cttactacac cctctgagcc agcatggaat ggaggatgag gacagagaag tcttaaagtg 8700 gaagtttgac agtcacctag cacacagaca catggcccgc gagctacatc cggagtatta 8760 taaagactgc tgacacagaa gggactttcc gctgggactt tccactgggg cggtccagga 8820 ggtgtggtct gggcgggacg gaggagtggc caaccctcag atgctgcata taagcagctg 8880 ctttttgcct gtactgggtc tctctgggta gaccagatct gagcctggga gctctctggc 8940 tatctaggga acccactgct taagcctcaa taaagcttgc cttgagtgct ct 8992 5 8966 DNA Human immunodeficiency virus type 1 isolate=“92NG003”; 157..1650gene“gag”; 4408..4986gene“vif”; 4926..5039gene“vpr”; 5184.7762tat; 5323..7967gene“rev”; 5425..5654gene“vpu”; 5572..8109gene“env”; 8111..8731gene“nef” 5 ttgaaagcga aagttaacag ggactcgaaa gcgaaagttc cagagaagtt ctctcgacgc 60 aggactcggc ttgctgaggt gcacacagca agaggcgaga gcggcgactg gtgagtacgc 120 caattttttt gactagcgga ggctagaagg agagagatgg gtgcgagagc gtcagtatta 180 agcgggggaa aattagatgc atgggaaaaa attcggttga ggccaggggg aaagaaaaaa 240 tatagaatga aacatttagt atgggcaagc agggaactgg agagatttgc acttaaccct 300 gacctcttag aaacaacaga aggttgtcag caaataatga gacagctgca accatctctc 360 cagacaggaa cagaggagat taaatcatta tttaatacag tagcaaccct ctattgtgta 420 catcaaagga tagaggtaaa agacaccaaa gaagctctag aggaagtgga aaaaatacaa 480 aagaacagtc agcaagaaac acagaaggca gcaatgggta aaggaaacag cagccaagtt 540 agccaaaatt atcctatagt gcagaatgca caagggcaag tggtacacca gcccatatca 600 cctaggactt taaatgcatg ggtaaaagta atagaagaaa agaacttcag tccagaagta 660 atacccatgt ttacagcatt atcagaagga gccaccccac aagatttgaa taccatgcta 720 aacaccgtgg gggggcatca agcagctatg caaatgctaa aagattctat taatgaagaa 780 gctgcagagt gggataggct acatccacaa caggcaggac ctattccacc aggccagata 840 agagaaccaa ggggaagtga tatagcagga actactagta ccctgcagga acaaataaca 900 tggatgacca gcaacccacc tatcccagtg ggagaaattt ataaaagatg gataattctg 960 gggttaaata aaatagtgag aatgtatagc cctgtcagta ttttagacat aaaacaaggg 1020 ccaaaagaac ccttcagaga ttatgtggat aggttcttta aaactttgag agctgagcaa 1080 gccacacagg aggtaaaaaa ctggatgaca gacaccttgt tggtccaaaa tgcgaaccca 1140 gattgtaaga ccatcctaag agcattagga gcaggagcta cactagaaga aatgttgaca 1200 gcatgtcaag gagtgggagg acccagccac aaagcaagag ttttagctga ggcaatgagc 1260 cgggcaacag gtacatcagc agccataatg atgcagaaaa acaattttaa gggcccgaga 1320 agaggtatta agtgtttcaa ctgtggcaag gaaggacatc tagccagaaa ttgcagggcc 1380 cctaggaaaa aaggctgttg gaaatgtgga aaggagggac atcaaatgaa agactgcaca 1440 gagagacagg ctaatttttt agggaaaatt tggccttcca acaaggggag gccagggaat 1500 tttcttcaga acaggccaga gccaacagcc ccacccgcag agagcttcgg gttcggagag 1560 gagatagccc cttccctgaa gcaggagccg agggaaaagg aatcacctcc attaacctcc 1620 ctcaaatcac tctttggcaa cgacccctag tcacagtaag aataggggga cagctaatag 1680 aagctctatt agacacagga gcagatgata cagtattaga acaaataaat ttaccaggaa 1740 aatggaaacc aaaaatgata gggggaattg gaggatttat caaagtaaaa cagtatgatc 1800 aaatacttat agaaattgaa gggaaaaagg ctatagggac agtactagta ggacctacac 1860 ctatcaacat aattgggaga aatatgttga ctcaaattgg ttgtacttta aattttccaa 1920 ttagtcctat tgagactgta ccagtaaaat taaaaccagg aatagatggc ccaaaggtta 1980 aacaatggcc attgacagaa gagaaaataa aagcattaac agaaatttgt acagatatgg 2040 aaaaggaagg aaaaatttca aaaattgggc cagaaaatcc atacaacact ccaatatttg 2100 ccataaagaa aaaagacagt actaaatgga gaaagttggt agatttcaga gagctcaata 2160 aaagaactca agacttctgg gaggtccaat taggcatacc tcatcccgcg gggttaaaaa 2220 agaaaagatc agtaacagta ctagatgtgg gggatgcata tttttcaatt cccctagatg 2280 aaaactttag aaagtataca gcattcacta tacctagtat aaataatgag acaccaggga 2340 ttagatatca gtacaatgtg cttccgcaag gatggaaagg atcaccagca atatttcaga 2400 gtagcatgac aaaaatctta gaacccttta gaacagaaaa tccagaaata gtgatctatc 2460 agtacatgga tgatttatat gtaggatctg acttagaaac agggcagcat agagcaaaaa 2520 tagaggaatt aagaaatcat ctactgagat ggggatttac cacaccagat aaaaaacatc 2580 agaaagaacc tccatttctc tggatgggat atgagctcca tcctgacaaa tggacggtac 2640 aacctataca gctgccaaac aaagaaagct ggactgtcaa tgatatacaa aaattagtgg 2700 gaaaactaaa ttgggcaagt cagatttatc cagggattaa agtaaagcaa ctatgtaaac 2760 tccttagggg ggccaaagca ctaacagaca tagtaccact gactgaagaa gcagaattag 2820 aattggcaga gaacagggaa attctaaaag aacctgtaca tggagtctac tatgacccat 2880 caaaagaatt aatagcagaa ttacagaaac aagggtgcga ccaatggaca tatcaaattt 2940 atcaagagcc atacaaaaat ctgaaaacag gaaagtatgc aaaaaggggg tctgcccaca 3000 ctaatgatgt aaaacagtta acagaagcag tgcaaaaaat agccacagag agcatagtaa 3060 tatggggaaa agttcctaaa tttaaactac ctataaggaa agaaacatgg gaagtatggt 3120 ggacagaata ttggcaggcc acctggattc ctgattggga gtttgtcaat acccctcctc 3180 tagtaaagtt atggtatcga ttagaaacag aacccatacc aggagcagaa acttactatg 3240 tagatggggc agctaataaa gaaacaaaat taggaaaggc aggatatgtt actgacagag 3300 gaaaacaaaa aattatcacc atacaggaaa caacaaatca aaaaactgaa ttacacgcaa 3360 ttcagctagc tttgcaggat tcaggatcag aagtaaacat agtaacagac tcacagtatg 3420 cattaggaat cattcaagca caaccagata ggagtgaatc agaattagtc aatcaaataa 3480 tagaacagct aataaaaaag gaaaaggtct acttaacatg ggtaccagca cacaaaggaa 3540 ttgggggaaa tgaacaagta gataaattag tcagtagtgg aatcagaaaa gtactgtttt 3600 tagatggcat agacaaagct caagaggacc atgaaagata tcacagcaat tggagagcaa 3660 tggctagtga ttttaatctg ccacctatag tagcaaaaga aatagtggcc agctgtgata 3720 aatgtcagct aaaaggggaa gccatgcatg gacaagtaga ctgtagtcca ggaatatggc 3780 aattagattg cacacatcta gaaggaaaag tcattatagt agcagtccat gtagccagtg 3840 gctatataga agcagaagtt atcccagcag aaacaggaca ggagacagca tacttcctgc 3900 taaaattagc aggaagatgg ccagtaaaag taatacacac agacaatggc agcaatttca 3960 ccagtgctgc aatgaaagca gcctgttggt gggcaaatat ccaacaggaa tttggaattc 4020 cctacaatcc ccaaagccaa ggagtagtgg aatctatgaa taaagaatta aagaaaatta 4080 tagggcaggt cagggatcaa gctgaacacc tcaagacagc agtacagatg gcagtattca 4140 ttcacaattt taaaagaaaa ggggggattg gggggtacag tgcaggggaa agaataatag 4200 acataatagc atcagatata caaactaaag aactacaaaa acagattata aaaattcaaa 4260 attttcgggt ctattacagg gacagcagag accccatttg gaaaggacca gcaaaactac 4320 tctggaaagg tgaaggggca gtagtaatac aggacaatag tgagataaag gtagtaccaa 4380 gaagaaaagt aaaaatcatt aaggattatg gaaaacagat ggcaggtggt gattgtgtgg 4440 caggtagaca ggatgaggat tagaacatgg aacagtttag taaaatatca tatgtataaa 4500 tctaagaaag ctaaggattg gttttataga catcactatg aaagtaggca tccaaaagta 4560 agttcagaag tacacatccc actaggggag gctagattag tagtaagaac atattggggt 4620 ctgcatacag gagaaagaga ctggcacttg ggtcaggggg tctccataga atggaagcag 4680 agaagatata gcacacaaat agatcctgac ctagcagacc aactgattca cctgcattat 4740 tttaactgtt tttcagaatc ggccgtaagg aaagccatac taggagaagt agttagacct 4800 aggtgtgaat atcaaacagg acataatcag gtaggatcac tacaatattt agcactcaaa 4860 gcattagtaa caccaacaca gacaaagcca cctttaccta gtgttaagaa gttaacagaa 4920 gatagatgga acgagcccca gaagaccagg ggccacagag ggagccattc aacgaatgga 4980 cactagaact gttagaagaa cttaaacatg aagctgttag acatggcttc atggattagg 5040 acaacatatt tataacacct atggggatac ttgggaagga gttgtagcta taataagaat 5100 attgcaacaa ctacttttta ttcatttcag aattgggtgt caacatagca gaataggcat 5160 tattccaggg agaagaggca ggaatggagc tggtagatcc tagcctagag ccctggaacc 5220 acccaggaag tcagcctaca actgcttgta acaaatgtta ctgtaaaata tgctgctggc 5280 attgccaatt gtgctttctg aacaagggct taggcatctc ctatggcagg aagaagcgga 5340 gacgccgacg aggaactcct cagagtcacc aggatcatca aaatcctgta ccaaagcagt 5400 gagtagtaat agttagtata tgtgatgcaa tccttagaaa tagctgcaat agcaggacta 5460 gtagtagcag ccatagcagc catagttgtg tggaccatag aaaaataaag aaacaggaga 5520 aaatagacag gttacttgat agaataagag aaagagcaga agatagtggc aatgagagtg 5580 aaggggacac agaggaattg gcaacacttg tggacatggt ggactttgat ccttgggttg 5640 gtgataattt gtagtgcctc aaataacttg tgggtcacag tctattatgg ggtaccagtg 5700 tgggaagacg cagatacccc tctattttgt gcatctgatg ctaaagcata tagtactgaa 5760 agacataatg tctgggccac acatgcctgt gtacccacag accccaaccc acaagagata 5820 actctggaaa atgtaacaga aacttttaac atgtggaaaa ataacatggt agaacagatg 5880 catgaggata taatcagttt atgggatgaa agcctaaagc catgtgtaaa gctaacccct 5940 ctctgtgtta ccttaaactg tactaatgtc aattgtaaca gtaatgtgac cagcactggg 6000 aacagtgctg ggaccaacgc tacgtgtaac atagaagaag caaacaactt aaaaaactgc 6060 tctttcaata taaccacaga aataagagat aagaaaaaga cagaatatgc gcttttctat 6120 agacttgatg tggtaccaat cgatggtaat aataatgtct caaataacta taggctaata 6180 aattgtaatg tctcaaccat taaacaagct tgtccaaagg tgtcttttga cccacttccc 6240 atacattatt gtgctccagc tgggtttgcg attttaaagt gtaggggtaa gaatttcact 6300 ggaacaggac aatgtaaaaa tgtcagttca gtacaatgta cacatggaat taaaccagtg 6360 gtatcaactc aattactact aaatggtagt ctagcagaag gagaaatagt aattagatct 6420 gaaaacctca cagacaatgc caaagtcata atagtacagc ttaataaaac tataggaatt 6480 aattgtacca gacccaacaa caatacaaga aaaagtataa gaatcggacc tggacaagcg 6540 ttctatgcaa caggtgaaat aataggacaa gaatggcagg agatgttaca gaaggtacag 6600 gcacaactag aacaggtctt taacaaaagt ataaccttta actcatccgc aggaggggac 6660 ctagaaatta caacacatag ttttaattgt agaggagaat ttttctattg taatacatca 6720 ggattgttta atgaatcagg agggaatgat accactatca cactcccatg taagataaaa 6780 caaattgtga gaatgtggca gagagtggga caagcaatgt atgcccctcc catcgcagga 6840 gatattacat gtagatcaaa cattacaggg ctattattaa caagagatgg tggggttaat 6900 aatactggaa atgagacctt cagacctgga ggaggagata tgagggacaa ttggagaagt 6960 gaattatata agtataaaat agtaaaaatt aaaccactag gaatagcacc caccaaggca 7020 aggagaagag tggtggagag aggaaaaagg gcagttggac tgggagctgt cttccttggg 7080 ttcttaggag cagcaggaag cactatgggc gcggggtcaa taacgctgac ggtacaggtc 7140 agacaattat tgtctggcat agtgcaacag caaagcaatt tgctgagggc tatagaggcg 7200 cagcaacatc tattgcaact cacagtctgg ggcattaaac agctccaggc aagagtcctg 7260 gctgtagaaa gatacctaaa ggatcaacag ctcctaggga tttggggctg ctctggaaaa 7320 ctcatctgca ccactaatgt gccttggaac actagttgga gtaataaatc ttatgaggag 7380 atttgggata acatgacctg gatacaatgg gaaagggaag tcagcaatta cacacaacaa 7440 atatacagcc taattgaaga atcgcagaac cagcaggaaa agaatgaaca agacttattg 7500 gcattggaca agtgggcaag tttgtggaac tggtttgaca taacaaaatg gctatggtat 7560 ataaaaatat ttataatgat agtaggaggt ttaataggtt taagaatagt ttttgctgtg 7620 ctttctatag taaatagagt taggcaggga tactcacctt tgtcattcca gacccttacc 7680 caccaccaga gggaacccga caggcccgaa agaatcgaag aaggaggtgg agagcaagac 7740 agagacagat cagtgcgctt agtgagcgga ttcttagcac ttgcctggga cgacctgcgg 7800 aacctgtgcc tcttcagcta ccaccgattg agagacttag tcttgattgc agcgaggaca 7860 gcagaactcc tgagacgcag cagtctccag ggactgagac tggggtggga gggcctcaaa 7920 tatctgtgga atctcctgtt gtattggggt cgggaactaa agaatagtgc tattaatttg 7980 attgatacaa tagcaatagc agtagctaac tggacagata gggttataga agtagcacaa 8040 ggagcttgta gagctattct caacatacct agaaggataa gacaaggctt ggaaagagct 8100 ttgctataaa ataggaggca agtggtcaaa aagtagcata gttggatggc ccgcggtaag 8160 ggagagaata agacaaaccc ctccagcaga aggagtagga gcagcacctc aagacttagc 8220 taggcatgga gcaatcacaa gcagcaatac agcacaaact aatcctgatt gtgcctggct 8280 agaagcacaa caggagaatt cagaggtagg ctttccagtc agacaacagg tacctttgag 8340 accaatgact tataaggctg cctttgatct cagcttcttt ttaaaagaaa aggggggact 8400 ggatgggcta atttactcta agaaaagaca agacatcctt gacctatggg tctataatac 8460 acaaggatac ttcccagatt ggcagaacta cactccaggg ccagggacta gattcccact 8520 gacatttcgg tggtgcttca aactagtacc aatggatcca gcagagatag aggaagccaa 8580 taaaggagag aacaacagtt tattacaccc tatctgccaa catggcctgg aagatgcgga 8640 cagagaagtg ctggtatgga gatttgacag tagcctagca cggagacaca tagcccgaga 8700 acaacatccg gagtactata aggactgctg acacagaagt tgctgacaca gatgttgctg 8760 acaaggggac tttccgcctg ggactttccg gggaggcgcg gcatgggagg gactggggag 8820 tggctaaccc tcagaagctg catataagca gccgcttctc gcctgtactg ggtctctctt 8880 gttagaccag atttgagcct gggagctctc tggctagcag gggaacccac tgcttaagcc 8940 tcaataaagc ttgccttgag tgcttc 8966 6 8954 DNA Human immunodeficiency virus type 1 isolate=93BR029; 142..1579gene=“gag”; 1437..4448gene=“pol”; 4393..4971gene=“vif”; 4911..5201gene=“vpr”; 5182..7782gene=“tat”; 5321..7972gene=“rev”; 5586..8114gene=“env”; 8116..8736gene=“nef” 6 ctgaaagcga aagtagaacc agaggagctc tcttgacgca ggactcggct tgctgaagcg 60 cgcacggcag gaggcgaggg gcggcgactg gtgagtacgc caaaaataaa atttggacta 120 gcggaggcta gaaggagaga gatgggtgcg agagcgtcag taataagcgg gggagaatta 180 gataaatggg aaaaaattag gttaaggcca ggaggacata aaaaatatag attaaaacat 240 atagtatggg caagcagggg agctagaacg attcgcagtt aatcctggcc ttttagagac 300 atcagaaggc tgtagacaaa tactggaaca gctacaacca gcccttaaga cgggatcaga 360 agaacttaga tcattatata atacagtagc aaccctctat tgtgtacatc aaaagataga 420 tgtaaaagac accaaggaag ctttagaaaa gatagaggaa gagcaaaaca aagtaagaaa 480 aaggcacagc aagcagcagc taacacagga aacaacagcc aggtcagcca aaattaccct 540 atagtgcaga accttcaggg gcaaatggta caccaggcca tatcacctag aactttaaat 600 gcatgggtaa aagtagtaga agagaaggct tttagcccag aagtaatacc catgttttca 660 gcattatcag aaggagccac cccacaagat ttaaacacca tgctaaacac agtgggggga 720 catcaagcag ctatgcaaat gttaaaagaa accatcaatg aggaagctgc agaatgggac 780 agagtacatc cagtgcatgc aggacctatc ccaccaggcc agatgaggga acctagggga 840 agtgatatag ctggaactac tagtaccctt caggaacaaa tacaatggat gacaagcaac 900 ccacctgtcc cagtgggaga aatttataaa agatggatca tcctaggatt aaataaaata 960 gtaagaatgt atagccctac cagcattctg ggcataagac aaggaccaaa ggaacccttt 1020 agagactatg tagatcgatt ttataaaact ctaagagcag agcaaacttc acaggatgta 1080 aaaaattgga tgacagaaac cttgttggtc caaaatgcga acccagattg caaaaccatt 1140 ttaaaagcat tgggaccagc agctacacta gaagaaatga tgacagcatg tcagggagtg 1200 gggggacccg gccataaagc aagagttttg gcagaagcaa tgagccaagt aacaaattca 1260 ggtaccataa tgatgcagag aggcaatttt aggaaccaaa gaaagactat taagtgtttc 1320 aattgtggca aagaagggca catagccaaa aattgcaggg cccctaggaa aaagggctgc 1380 tggaaatgtg gaaaggaagg acaccagatg aaagattgta ctgagagaca ggctaatttt 1440 ttagggaaaa tctggccttc ccacaaggga aggccaggga atttccttca gagcagacca 1500 gagccaacag ccccaccagc agagagcttc aggtttgggg aagaggtaac aactccctct 1560 cagaaacagg agccgataga caaggagatg tatcctttgg cttccctcag atcactcttt 1620 ggcaacgacc cctcgtcaca gtaaagatag gggggcaact aaaggaagcc ctattagata 1680 ccggagcaga tgatacagta ttagaagaaa taaatttacc aggaagatgg aaaccaaaaa 1740 tgataggggg aattggaggt tttatcaaag taagacagta tgatcaaata cccatagaaa 1800 tttgtggacg taaagctaca ggtacagtat tagtaggacc tacacctgtc aacataattg 1860 gaagaaatct gttgactcag attggctgca ctttaaattt tcccattagt cctattgaaa 1920 ctgtaccagt aaaattgaag ccaggaatgg atggcccaag ggttaaacaa tggccattga 1980 cagaagaaaa aataaaagca ttaacagaaa tatgtacaga aatggaaaaa gaaggaaaaa 2040 tttcaaaaat tgggcccgaa aatccataca atactccagt atttgccata aagaaaaaag 2100 atagtactaa atggagaaaa ttagtagatt tcagagaact taataagaga actcaagact 2160 tctgggaagt tcagttaggg ataccacatc ccgcagggtt aaagaagaaa aaatcagtaa 2220 cagtactgga tgtgggtgat gcatattttt cagttccatt agataaagac ttcaggaagt 2280 atactgcatt taccatacct agtacaaaca atgaaacacc agggcttaga tatcagtaca 2340 atgtgcttcc acaggggtgg aaaggatcac cagcaatatt ccaaagtagc atgacaaaaa 2400 tcttagagcc ttttagaaaa caaaatccag acatagttat ctatcaatac atggatgatt 2460 tgtatgtagg atctgactta gaaatagggc agcatagaac taagatagag gaattgagac 2520 agcatttgtt gaggtgggga tttaccacac cagacaaaaa acatcagaaa gaacctccat 2580 tcctttggat gggttatgaa ctccatcctg ataaatggac agtacagcct atagtgctgc 2640 cagaaaaaga cagctggact gtcaatgaca tacagaagtt agtgggaaaa ttgaattggg 2700 caagtcagat ttatgcaggg attaaagtaa ggcaattatg taaactcctt aggggaacca 2760 aagcactaac agaagtagta ccactaacag cagaggcaga gctagaactg gcagaaaaca 2820 gggagattct aaaagaacca gtacatggag tgtattatga cccctcaaaa gacttaatag 2880 cagaaataca gaaacagggg caaggccaat ggacatatca aatttatcaa gagccatata 2940 aaaatttgaa aacaggaaag tatgcaagga tgaggggtgc ccacactaat gatgtaaaac 3000 aactaacaga ggcagtgcaa aaaataacca cagaaagcat agtaatatgg ggaaagattc 3060 ctaaatttaa actacccata caaaaagaaa cgtgggaagc atggtggata gagtattggc 3120 aagccacctg gattcctgag tgggagtttg tcaatacccc tcccttagtg aaattatggt 3180 accagttaga gaaagaaccc atagtaggag cagaaacttt ctatgtagat ggggcagcta 3240 atagggaaac taaattagga aaagcaggat atgtgactga cagaggaaga caaaaagttg 3300 tccccctaac ggacacaaca aatcagaaaa ctgagttaca agcaattcat ctagctttgc 3360 aggattcggg attagaagta aacatagtaa cagactcaca atatgcatta ggaatcattc 3420 aagcacaacc agataagagt gaattagaaa tagtcaatca aataatagag cagttaataa 3480 aaaaggaaaa gatctacctg gcatgggtac cagcacacaa aggaattgga ggaaatgaac 3540 aagtagacaa attagtcagt tctggaatca ggaaagtact atttttagat ggaatagata 3600 aggcccaaga agaacatgag aaatatcaca ataattggag agcaatggct agtgacttta 3660 acataccacc tgtagtagca aaagaaatag tagccagctg tgataaatgt cagctaaaag 3720 gagaagccat gcatggacaa gtagactgta gtccaggaat atggcagcta gattgtacac 3780 acttagaagg aaaagttatc ctggtagcag tgcatgtagc cggtggatat atagaagcag 3840 aagttattcc agcagagaca gggcaagaaa cagcatactt tctcttaaaa ttagcaggaa 3900 gatggccagt aaaaacaata cacacagaca atggcagcaa tttcaccagt actacagtca 3960 aggccgcctg ttggtgggcg gggatcaagc aggaatttgg cattccctac aatccccaaa 4020 gtcaaggagt aatagaatct atgaataaag aattaaagaa aattatagga caggtaaggg 4080 atcaggctga acatcttaag acagcagtac aaacggcagt attcatccac aattttaaaa 4140 gaaaaggggg gattgggggg tacagtgcag gggaaagaat agtagacata atagcaacag 4200 acatacagac taaagaatta caaaaacaaa ttacaaaaat tcaaaatttt cgggtttatt 4260 acagagacag cagagatcca ctttggaaag gaccagcaaa gcttctctgg aaaggtgaag 4320 gggcagtagt aatacaagat aatagtgaca taaaagtagt gccaagaaga aaagtaaaga 4380 tcattaggga ttatggaaaa cagatggcag gtggtgattg tgtggcaggt agacaggatg 4440 aggattaaca catggaaaag tttagtaaaa taccatatgc atgtttcaaa gaaagccaaa 4500 agatggtttt atagacatca ctttgaaagc aggcatccaa gagtaagttc agaagtacat 4560 atcccactag aggaagctaa attagtaata acaacatatt gggggctgca tacaggagaa 4620 agagattggc atctgggtca gggagtctcc atagaatgga ggcaggggag gtataggaca 4680 caaatagacc ctggcctggc agaccaactg atccatatat attattttga ttgtttttca 4740 gaatctgcca taaggaaagc catattagga catagaatta gccctaggtg tgattatcaa 4800 gcaggacata acaaggtagg atctctacag tacttggcac taacagcatt aataaaacca 4860 aaaaagagaa agccaccttt gcccagtgtt aagaaactga cagaggatag atggaacaag 4920 ccccagaaga ccaaggacca cagagggagc catacaatga atggacacta gaacttttag 4980 aggaacttaa gagtgaagct gttagacatt ttcctaggtt atggctccat agcttaggac 5040 aacatatcta tgaaacttat ggggatactt gggcaggagt ggaagccata ataagaattc 5100 tgcaacaact gctgtttatt catttcagaa ttggatgtca acatagcaga ataggcatta 5160 atcgacagag gagagcaagg aatggagcca gtagatccta gactagagcc ctggaagcat 5220 ccaggaagtc ggcctcagac ggcttgtaat agttgctatt gtaaaaagtg ttgctttcat 5280 tgtcaagttt gtttcacaac aaagggctta ggcatctcct atggcaggaa gaagcggaga 5340 cagcgacaca gaactcctca aagcagtcag ctacatcaag atcctgtacc aaagcagtaa 5400 gtattgttaa gtaatatatg taatgtcata tttgttagta ataggtttag cagcattaat 5460 agcagcacta ataatagcaa tagttgtgtg gactatagca tatatagaat atagggaact 5520 agtaaggcaa agaaaaataa ataggttata taaaagaata agagaaagag cagaagacag 5580 tggcaatgag agtgaggggg atgcagagga attggcagca cttggggaaa tggggccttt 5640 tattcctggg gatattgata atctgtaatg ctgaaaactt gtgggtcaca gtctattatg 5700 gggtacctgt gtggaaagaa gcaaccacta ctttattctg tgcatcagat gctaaagcat 5760 atgaaaaaga agcacataat gtctgggcta cacatgcctg tgtacccaca gatcccaatc 5820 cacaagaagt agttctggaa aatgtaacag aaaattttga tatgtggaaa aataacatgg 5880 tagaacaaat gcatacagat ataatcagtt tatgggatca aagcctgaag ccatgtgtga 5940 agttaacccc actctgtgtt actttacgtt gtagtaatgc cactaccaac agtactcaaa 6000 acgacaccct gaaggaagag ccaggggcaa tacaaaactg ttctttcaat atgaccacag 6060 aagtaagaga taagcagctg aaagtacatg cactttttta taggcttgat atagtaccaa 6120 tcagcaatga taatagtagc aatgataata gtagcagaga atacaggcta ataaattgta 6180 atacctcaac ccttacacag gcttgtccaa aggtatcttg ggatccaatt cccatacatt 6240 attgtgctcc agctgggtat gcgattctaa agtgtaatga taaaaaattc aatgggacgg 6300 ggccatgcag gaatgtcagc acagtacaat gtacacatgg aattaaacca gtggtatcaa 6360 ctcaattgtt gttaaatggc agcctagcag aaaaagatat aataatcaga tctcaaaata 6420 tctcagataa tgcaaaaacc ataatagtac aacttaatgt atctgtgccg attaattgta 6480 caagacccaa caacaataca agaaaaagta taccaatagg accaggacga gcattttata 6540 caacaggaga aataatagga gacatcagaa aggcacattg taacgttagt ggaacaaaat 6600 ggaatgagac gttagaaaag gtaagggcaa agttaaagcc tcatttccct aatgcaacaa 6660 taaaatttaa ctcatcctca ggaggggacc tagaaattac aatgcatagt tttaattgta 6720 gaggagaatt tttctactgc aatacatcag gactgtttaa tgacacagta gacaatggca 6780 ctatcactct cccatgtcga ataaagcaaa ttgtaaatat gtggcaggaa gtggggcgag 6840 caatgtatgc cgctcccatt gcaggaaaca ttacctgtag ctcaaatatt acaggtctac 6900 tattgacaag agatggtggt cagaataatc agacggagga gaccttcaga cctgggggag 6960 gaaatatgaa agacaactgg agaagtgaat tatataaata taaagtagta gaaattgagc 7020 cattaggagt agcacccacc aaggcaaaaa gacaagtggt gaagagagaa aaaagagcag 7080 tgggaatggg agctttgttc cttgggttct tgggagcagc aggaagcact atgggcgcag 7140 cgtcaataac gctgacggca caggccagac aattattgtc tggcatagtg caacagcaga 7200 ataatttgct gagggctatt gaagcgcaac agcatctgtt gcagctcaca gtctggggca 7260 ttaaacagct ccaggcaaga atcctggctg tggaaagata cctaaaggat caacagctcc 7320 tagggctttg gggctgctct ggaaaactca tctgcaccac tgatgtgccc tggaactcta 7380 gttggagtaa caaatctcag gagaagatct gggggaacat gacctggatg gagtgggaaa 7440 aagagattag caattactca aacgaaatat ataggttaat tgaagagtcg cagaaccagc 7500 aggaaaagaa tgaacaagaa ttattggcat tggacaaatg ggcaagtctg tggaattggt 7560 ttgacatatc aaaatggctg tggtatataa aaatattcat aatgatagta ggaggcttga 7620 taggcttaag aatagttttt gctgtgcttt ctatagtaaa tagagttagg aagggatact 7680 cacctttgtc attacagacc cgcttcccaa gcccaaggga acccgacagg cccgaaggaa 7740 tcgaagaagg aggtggagag ccaggcaaag acagatccgt gagattagtg aacggattct 7800 tagctcttgt ctgggacgac ctgaggaacc tgtgcctctt cagctaccgc cacttgagag 7860 acttcatatt aattgcagcg aggattgtgg acaggggact gaagaggggg tgggaagccc 7920 tcaaacttct ggggaatctc gcgctgtatt ggagtcagga actaaagaat agtgctatta 7980 gcttgcttaa taccacagca atagtagtag ctgaggggac agatagagtt atagaagctt 8040 tgcaaagagc gggtagagct gttcttaacg tacctagaag aataagacag ggcttggaaa 8100 gggctttgct ataaaatggg tagcaagtgg tcaaaaagta gtatagttgg gtggcctgct 8160 ataagggaaa gattaagaca aacccctcca gcagcagaag gggtgggagc agtgtctcaa 8220 gacttagaaa gacggggggc aattacaagc agcaatactg gagctaataa tcctgacttg 8280 gcctggctgg aggcacaaga ggaagaggaa gtaggctttc cagtcagacc tcaggtacct 8340 ttaagaccaa tgacttataa gggagctctt gatctcagtc actttttaaa agaaaagggg 8400 ggactggaag ggttaattta ttccaagaaa agacaagaga tccttgatct gtgggtttac 8460 cacacacaag gctacttccc tgattggcag aactacacac cagggccagg gaccagatat 8520 ccactgacct tagggtggtg cttcaagcta gtaccagttg acccagagga ggtagaaaag 8580 gccaatgaag gagagaacaa ctgcttgcta caccccatga gccaacatgg aatggaggat 8640 gaagacagag aaatactgca gtggaggttt gacagccgcc tagcatttca tcacatggcc 8700 cgagagctgc atccggagta ctacaaggac tgctgacatt gagttttcta caagggactt 8760 tccgctgggg actttccagg gaggtgtggc ctgggcggga ctggggagtg gcgagccctc 8820 agatgctgca tataagcagc tgctttctgc ctgtactggg tctctctggt tagaccagat 8880 ttgagcctgg gagctctctg gctagctagg gaacctactg cttaagcctc aataaagctt 8940 gccttgagtg ctta 8954 7 9050 DNA Human immunodeficiency virus type 1 isolate=“94CY032.3”; 156..1658“gag”; 1454..4 462“pol”; 4407..4985“vif”; 4925..5212“vpr”; 5200..7842“tat”; 5339..8026“rev”; 5435..5680“vpu”; 5598..8168“env”; 8170.8829“nef” 7 ttgaaagtga aagttaatag gactcgaaag cgaaagttcc agagaagttc tctcgacgca 60 ggactcggct tgctgaggtg cacacagcaa gaggcgagag cggcgactgg tgagtacgcc 120 aaattttttg actagcggag gctagaagga gagagatggg tgcgagagcg tcagtattaa 180 gtgggggaaa attagatgca tgggagagga ttcggttaag gccaggggga aagaaaaaat 240 atagactgaa acatctagta tgggcaagca gagagttgga aagattcgca cttaaccctg 300 gccttttaga aacagcagaa ggatgtcaac aattaatgga acagttacaa tcaactctca 360 aaacaggatc agaagaactt agatcattat ataatactat aacaaccctc tggtgcgtac 420 atcaaagaat agatgtacaa gacaccaagg aagctttaga taaaatagag gaaatacaaa 480 gtaagagcaa gcaaaagaca cagcaggcag cagctgccgc aggaggtagc agcaatgtca 540 gccaaaatta ccctatagtg caaaatgcac aagggcaaat ggtacatcag agcatttcac 600 ctagaacttt gaatgcatgg gtaaaagtaa tagaagaaaa ggctttcagc ccagaagtaa 660 tacccatgtt ctcagcatta tcagagggag ccaccccaca agatttgaac atgatgctaa 720 atatagtggg gggacaccag gcagcaatgc aaatgttaaa agataccatc aatgaggaag 780 ctgcagactg ggacaggaca catccagtac atgcagggcc tattccacca ggccagatga 840 gagaaccaag gggaagtgat atagcaggaa ctactagtac ccttcaagaa caaataggat 900 ggatgacaag caacccacct gtcccagtgg gagaaatcta taaaagatgg ataatcttgg 960 ggttaaataa aatagtaaga acgtatagcc ccattagcat cttggacata agacaaggac 1020 caaaagaacc cttcagagat tatgtagata ggttctttaa atgtctcaga gcagaacaag 1080 ctacccagga ggtgaaaaat tggatgacag aaaccctgct ggtccaaaat gcgaatccag 1140 actgtaagtc catcttaaaa gcattaggaa caggggctac attagaagaa atgatgacag 1200 catgtcaggg agtgggagga cccagccata aagcaagagt tttagctgag gcaatgagcc 1260 aggcatcaaa tgcagcagca gccataatga tgcagaaaag caaatttaag ggccaaagaa 1320 gaactattaa gtgtttcaac tgtggcaagg aaggacatct agccagaaat tgcagggccc 1380 ctaggaaaaa gggctgctgg aagtgtggaa aggagggaca tcaaatgaaa gactgcactg 1440 agagacaggc taatttttta gggagaatgt ggccttccag caaagggagg ccaggaaatt 1500 ttcttcagaa caggccagag ccaacagccc cgcccgcgga atgcttagag aggaaagagg 1560 agacaacctc ctctctgaag caggaaccga gggacaagga actatatcct ttaacttccc 1620 tcaaatcact ctttggcagc gaccccttgt cacaataaaa ctagggggac agataaggga 1680 ggctctttta gatacaggag cagatgatac agtattagaa gaaataaatt tgccaggaaa 1740 atggaagcca aaaatgatag ggggaatcgg aggttttatc aaagtaagac aatatgatca 1800 gatacctata gaaatttgtg gaaaaaaggc cataggcaca gtgttagtag gacctacacc 1860 tgtcaacata attggacgaa acatgttgac tcagcttggt tgtactttaa attttccaat 1920 tagtcctatt gaaactgtac cagtaaaatt aaagccagga atggatggcc caaaggttaa 1980 acaatggcca ttgacagaag aaaaaataaa agccttaaca gagatatgta cagacatgga 2040 aaaggaaggc aagatttcaa aaattgggcc tgaaaatcca tacaatactc caatatttgc 2100 tataaagaaa aaagacagca ctaaatggag aaaattagta gatttcagag aactcaataa 2160 aagaactcag gacttctggg aagttcagtt aggaataccg cacccagcag ggttaaagaa 2220 gaaaaaatca gtaacagtat tggatgtggg ggatgcatat ttttcagttc ccttagatcc 2280 agagttcagg aagtacactg cattcaccat acctagtacc aacaatgaga caccaggaat 2340 tagatatcag tacaatgtgc ttccacaggg ctggaaagga tcaccagcaa tattccaatg 2400 tagcatgaca aaaatcttag agccctttag attcaaaaac ccagaaatag tcatatacca 2460 atatatggat gatttgtatg tagggtctga cttagaaata gggcaacata gagcaaaaat 2520 agaagagcta agagagcatc tattgagatg gggattcacc acaccagaca aaaaacatca 2580 gaaagaaccc ccatttcttt ggatggggta tgaactccat cctgacaaat ggacagtgca 2640 gcctatacaa ccggcagaaa aggatagctg gactgtcaac gatatccaga agttagtggg 2700 aaaactaaat tgggcaagtc agatttatcc agggattaaa gtaaagcaat tatgtaaact 2760 tcttagggga gctaaagccc taacagacat agtaccacta actacagagg cagagttaga 2820 attagcagag aacagggaga ttctaaaaga accagtacat ggggcatatt atgacccatc 2880 aaaagactta atagcagaaa tacagaagca agggcaaggt caatggacat atcaaatata 2940 tcaagagcca cataaaaatc tgaaaacagg gaagtatgca agaaccagat ctgcccacac 3000 taatgatgtt agacaattaa cagaagcagt gcaaaagata gccatggaat gcatagtaat 3060 atggggaaag actcctaagt ttagattacc catacaaaag gaaacatggg acacatggtg 3120 gacagaatat tggcaggcca cctggatccc tgaatgggaa tttgtcaata cccctcctct 3180 agtaaaatta tggtaccagt tagaaacaga ccccatagca ggagcagaaa ctttctatgt 3240 agatggggca gctaatagag aaacaaaaca gggaaaagca ggatatgtta ctgatagagg 3300 cagacaaaaa gttgtctccc tatctgaaac aacaaatcag aagactgaat tacaagcaat 3360 ttacttagct ttgcaggatt caggatcaga agtaaacata gtaacagact cacagtatgc 3420 aataggaatc attcaagcac aaccagatag aagtgaatca gatttagtta atcaaataat 3480 agagcagtta atacggaagg acaaggtcta cctgtcatgg gtaccagcac acaaagggat 3540 tggaggaaat gaacaagtag ataaattagt cagcaatgga atcagaaagg tgctattttt 3600 agatggaata gataaggctc aagaagaaca tgagaaatat cacaataact ggagagcaat 3660 ggctagtgat tttaatctgc catcagtggt agcaaaagag atagtagcta gctgtaataa 3720 atgtcagcta aaaggggaag ccatgcatgg acaagtggac tgtagtccag ggatatggca 3780 gttagattgt acacatttag aaggtaaagt tatcatggta gcagttcatg tggctagtgg 3840 atacatagaa gcagaagtta tcccagcaga aacaggacag gaaacagcct acttcatact 3900 aaaattagca ggaagatggc cagtgaaaat gatacatgca gacaacggcc ccaatttcac 3960 cagtgctgcg gttaaggcag cctgttggtg ggcagatatc aaccaggaat ttggaattcc 4020 ctacaatccc caaagccaag gagtagtgga atctatgaat aaagaattaa agaaaatcat 4080 agggcaggtc agggatcaag ctgaacacct taagacagca gtacagatgg cagtattcat 4140 tcacaatttt aaaagaaaag gggggattgg ggggtacagt gcaggggaaa gaataataga 4200 cataatagca tcagatatac aaactaaaga actacaaaaa caaattacaa aaattcaaaa 4260 ttttcgggtt tattacaggg acagcagaga accaatttgg aagggaccag caaaactact 4320 ctggaaaggt gaaggggcag tagtaataca ggacaacagt gatatcaaag tagtaccaag 4380 aagaaaagca aagattatta gggactatgg caaacagatg gcaggtaatg attgtgtggc 4440 aggtagacag gatgaagatt agaacatgga acagtctagt gaaacatcat atgtatgttt 4500 caaagaaagc taaaggatga ttctatagac atcactatga aagtaggcac ccaaaagtaa 4560 gttcagaagt acatatccca ctaggggagg ctagattagt agtaagaaca tattggggtc 4620 tgcagccagg ggaacaagac tggcacttgg gtcatggagt ctccatagaa tggaggctca 4680 gaagatatag cacacaagtg gatcctgacc tggcagacca actaattcat atgcattact 4740 ttgattgttt ttcagaatct gccataagga aagccatatt aggacataga gttagtccta 4800 ggtgtgaata tcaagcagga cataataagg taggatcctt acaatacctg gcactagcag 4860 cattaatatc cccaaaaaag acaaagccac ctttgcctag tgttaagaaa ctagtggagg 4920 atagatggaa caagccccag aagaccaggg gccgcagaga gaaccaaata atgaatggac 4980 actagagctt ttggaggagc ttaaaaatga agctgttagg cattttccta gaccctggct 5040 ccatggccta ggacagcata tctataacac ttatggagat acctgggaag gggttgaagc 5100 tataataaga attttgcaac aactactgtt tattcatttc agaattgggt gccaacatag 5160 tagaataggc attactcctc aaaggagaag aggcagggga tggagccagt agatcctgac 5220 ctagagccct ggaaccatcc gggaagtcag cctacaactg attgtaacaa gtgtttctgt 5280 aaaaagtgtt gctggcattg ccaagtttgc tttctgaaaa aaggcttagg catctcctat 5340 ggcaggaaga agcggaaaca tcgacgagga tctcttcaag gcagcaaggg ccatcaaaat 5400 cttataccaa agcagtaagt attaagtata tgtaatgtta ttctgggaaa tctgggcaat 5460 agtaggactg gtagtagcgc taattatagt aatagtagtg tggactttag tatttataga 5520 atataagaaa ttgagaaggc aaaggagaat agacagcttg tacaatagaa taagagaaag 5580 agcagaagac agtggcaatg agagtgatgg ggatgcagag gaattatcca cacttgtggg 5640 aatggggaac tttgatcctt gggttggtga taatctgtag tgcctcaaac aacttgtggg 5700 tcacagttta ttatggggta cctgtgtgga gagacgcaga gaccacccta ttttgtgcat 5760 cagaagctaa agcatatgag aaagaagtac ataatatctg ggctacacat gcctgtgtac 5820 ccacagaccc caacccacaa gaagtagctc tgataaatgt aacagagaac tttaacatgt 5880 ggaaaaatga catggtagaa cagatgcatg aggatataat cagtttatgg aatgaaggcc 5940 taaaaccatg tgcaaagcta acctctctct gtgttacttt tacatgtatt aatgcaacta 6000 ctactaatag taccaatggc actgtgatta aagaaggaat aaaaaactgc tctttcgata 6060 taaccacaga aataagggat aagaagaaga aagaatatgc gcttttctat agaattgata 6120 tagtgccaat taatgctaga gtgccaatta atggtagtaa taggaataat agtacagaag 6180 agtatatgtt aataaattgt aacgcctcaa ccattaaaca ggcttgccca aaggtgtctt 6240 ttgagccaat tcccatacat tattgtgccc cagctggttt tgcaatttta aagtgtaatg 6300 agaaaaattt cactggatta gggccatgca caaatgtcag ctcggtacga tgcactcatg 6360 gaattaagcc agtggtatca actcaattgc tgttaaatgg aagcttagca acggaagagg 6420 tagtaattag atctaaaaat atcacagaca ataccaaaaa tataatagta cagcttgcaa 6480 aggctgtaaa aattaattgt accagacctg gcaacaatac aagaaaaagt gtacatatag 6540 ggccaggact aacatggtat gcaacaggtg aaataatagg agatataaga caagcacatt 6600 gtaacattag tggaaatgat tggaatgaca ccttaaaagt gataagtgaa gaattgaaaa 6660 gactcttccc taataaaaca ataaaatttg ctccacccgt aggaggggac ctagaaatta 6720 caacacatag ctttaattgt aaaggagaat ttttctattg caatacaaca ccactgttta 6780 atagtacaca catgcaaaat ggtacaaaca ttacaagtac agattctaca aattcaacca 6840 tcacactcca atgcagacta aaacaatttg taaggatgtg gcaggaagtg gggcaagcaa 6900 tgtacgcctc ccccattgca gggagcatta actgcagctc agatattaca ggaataatat 6960 tgacaagaga tggtggtact aataatactg agatcttcag acctggagga ggagacatga 7020 gggacaattg gagaagtgaa ctatataaat ataaagtagt aaagattgaa ccaataggag 7080 tagcacccaa taaggcaagg agacgagtgg tgcagagaga aaaatgagca gtgggaatag 7140 gggccatgtt ccttgggttc ttgggagcag caggaagcac tatgggcgca gcgtcaatga 7200 cgctgacggt acaggccaga caattattgt ccggcatagt gcagcagcag agcaatttgc 7260 tgagggctat agaggctcaa caacatctgt tgagactcac ggtctggggc attaaacagc 7320 tccaggcaag agtcctggct ctggaaagct acctaaagga tcaacagctc ctaggaattt 7380 ggggctgctc tggaaaactc atctgcacca ctaatgtacc ttggaactct agttggagta 7440 ataaatctta taatgatata tgggacaata tgacctggtt gcaatgggat aaagaaatta 7500 acaattacac acaaataata tatgggttac ttgaagaatc acagaaccag caggaaaaga 7560 atgagcaaga cttattggcc ttggacaagt gggcaagcct gtggaattgg tttagcataa 7620 caaaatggct atggtatata aaaatattta taatgatagt aggaggcttg ataggcttaa 7680 gaataatttt tgctgtgctt tctatagtaa atagagttag gcagggatac tcacctttgt 7740 ctttgcagac ccttatccca acaacccaac ggggactcga caggcccgga ggaacagaag 7800 aagaaggtgg cgagcaagac agaagcagat ccattcgctt agtgaacgga ttcttgccac 7860 ttatctggga cgacctgcgg aacctgtgcc tcttcagcta ccgccacttg agaaacttac 7920 tcttaattgt agcgaggact gtggaacttc tggggataag ggggtgggaa gccctcaagt 7980 atctgtggaa cttcctgctg tattggggac aggagctaaa gaatagtgct attaatttgt 8040 ttaataccac agcaatagca gtagctgagg gaacagatag gattatagaa gcagtacaga 8100 gagcttgtag agctatttgc aacataccta gaagaatcag acagggcctt gaaagagctt 8160 tgctttaaaa tgggaggcaa atggtcaaaa agtagcatag ttggatggcc tgagataagg 8220 gaaagaatga ggcgagctcg agctgagcca gaaagaatga ggcgagctca agctgagcca 8280 gcagcagcag gagtaggagc agtgtctcaa gacttggaca aacatggggc aatcacaatt 8340 aacaatacag cagctactaa tcctgacaaa acctggctgg aagcacaaga agaggaagaa 8400 gaggtaggtt ttccagtcag gccacaggta cctttaaggc caatgacctt taaaggagct 8460 ttagatctca gccacttttt aaaagaaaag gggggactgg atgggctaat ttactccaag 8520 aaaagacaag agatccttga tctgtgggtc tatcacacac aaggtttctt ccctgattgg 8580 gataactaca caccaggacc aggggagaga ttcccactgt gctttggatg gtgcttcaag 8640 ctagtaccag tagatccaca ggaggtggaa gaggccactg aaggagagaa cacctgtttg 8700 ctgcacccta taagccagca tggaatggag gatgaagaga gagaagtatt aaagtggaag 8760 tttgacagtc gcctggcata caagcacgta gcccgagagc tgcatccgga gttttacaaa 8820 gactgctgac acagaagttg ctgacaaagg gactttccgc ccgggacttt ccaggggagg 8880 cgcggcctgg gaggggttgg ggagtggcta accctcagat gctgcataaa agcagccgct 8940 tctcgcctgt actgggtctc tctggttaga ccagatctga gcctgggagc tctctggcta 9000 gctagggaac ccactgctta agcctcaata aagcttgcct tgagtgcttc 9050 8 9010 DNA Human immunodeficiency virus type 1 isolate=96ZM651; 137..1621“gag”; 1426..4425“pol”; 4370..4948“vif”; 4888..5178“vpr”; 5159..5373-7734..7824“tat”; 5298..5373-7734..7981“rev”; 5387..5647“vpu”; 5565..8171“env”; 8173..8793“nef” 8 cttgaagcga aagtagacca gaggagatct ctcgacgcag gactcggctt gctgaagtgc 60 actcggcaag aggcgagagc ggcggctggt gagtacgcca aattttattt gactagcgga 120 ggctagaagg agagagatgg gtgcgagagc gtcaatatta agagggggaa aattagataa 180 atgggaaaaa attaggctaa ggccaggggg aaagaaacgc tatatgataa aacacctagt 240 atgggcaagc agggagctgg aaagatttgc gcttaaccct ggccttttag aaacatcaga 300 aggctgtaaa caaataatga aacagctaca accagctctt cagacaggaa cggaggaact 360 tagatcatta tacaacacag tagcaactct ctattgtgta catgaagggg tagaggtacg 420 agacaccaag gaagccttag acaggataga ggaagaacaa aacaaaattc agcaaaaaat 480 acagcaaaaa acacagcaag cggctgacgg aaaggtcagt caaaattatc ctatagtgca 540 gaatctccaa gggcaaatgg tacaccagaa actatcacct agaactttga atgcatgggt 600 aaaagtaata gaagaaaaag cttttagccc agaggtaata cccatgttta cagcattatc 660 agaaggagcc accccacaag atttaaacac catgttaaat acagtggggg gacatcaagc 720 agccatgcaa atgttaaaag atactatcaa tgaggaggct gcagaatggg atagattaca 780 tccagtgcat gcagggccta ttgcaccagg ccaaatgaga gaaccaaggg gaagtgatat 840 agcaggaact actagtaccc tccaagaaca gatagcatgg atgacaagta atccccctat 900 tccagtggga gacatctata aaagatggat aattctgggg ttaaataaaa tagtaagaat 960 gtatagccct gtcagcattt tggacataaa acaagggcca aaggaaccct ttagagacta 1020 tgtagaccgg ttcttcaaaa ctttaagagc tgaacaggct acacaagaag taaaaaattg 1080 gatgacagac accttgttgg tccaaaatgc aaacccagat tgcaagacca ttttaaaagc 1140 attaggacca ggggctacat tagaagaaat gatgacagca tgtcaaggag tgggaggacc 1200 tagccacaaa gcaagagtgt tggctgaggc aatgagccaa acaaatagtg taaacatact 1260 gatgcagaaa agcaatttta aaggaaataa aagaatggtt aaatgtttta actgtggtaa 1320 ggaagggcac atagccagaa attgcagggc ccctaggaaa aagggctgtt ggaaatgtgg 1380 aaaggaggga caccaaatga aagactgtac tgagaggcag gctaattttt tagggaaaat 1440 ttggccttcc cacaagggaa ggccagggaa tttccttcag aacaggccag agccaacagc 1500 cccaccagca gagagcttca ggttcgagga gacaaccccc gctccgaagc aggagtcgaa 1560 agacagggaa gccttaactt ccctcaaatc actctttggc agcgacccct tgtctcaata 1620 aaggtagggg gccaaataaa ggaggctctc ttagacacgg gagcaggtga tacagtatta 1680 gaagaaataa atttgccagg caaatggaaa ccaaaaatga taggaggaat tggaggcttt 1740 atcgaagtaa gacaatatga tcaaatacct atggaaattt gtggaaaaaa ggctataggt 1800 acagtattag taggacctac acctgtcaac ataattggaa gaaatatgtt gactcagctt 1860 ggatgcacac taaattttcc aattagtcct attgaaactg taccagtaaa attaaagcca 1920 ggaatggatg gcccaaaggt taaacaatgg ccattgacag aagagaaaat aaaagcttta 1980 acagcaattt gtgaagaaat ggagaaggaa ggaaaaatta caaaaattgg gcctgaaaat 2040 ccatataaca ctccagtatt tgccataaaa aagaaggaca gtactaagtg gcgaaaatta 2100 gtagatttca gggaactcaa taaaagaact caagactttt gggaagttca attaggaata 2160 ccacacccag cagggttaaa aaagaaaaaa tcagtgacag tactggatgt gggggatgca 2220 tatttttcag ttcctttaga tgaaagcttc aggaaatata ctgcattcac catacctagt 2280 acaaacaatg aaacaccagg gattagatat caatataatg tgcttccaca gggatggaaa 2340 ggatcaccag caatattcca gagtagcatg acaaaaatct tagagccctt cagggcacaa 2400 aatccagaca tagtcatcta tcaatatatg gatgacctgt atgtaggatc tgacttagaa 2460 atagggcaac atagagcaaa aatagaagag ttaagagaac atctattaaa gtggggattt 2520 accacaccag acaagaaaca tcagaaagaa cccccatttc tttggatggg gtatgaactc 2580 catcctgaca aatggacagt acagcctata cagctggcag aaaaagatag ctggactgtt 2640 aatgatatac agaagttagt gggaaaatta aactgggcaa gtcagattta cgcagggatt 2700 aaagtaaggc aactttgtaa actccttagg ggagccaaag cactaacaga catagtacca 2760 ctaactgaag aagcagaatt agaattggca gagaacaagg aaattttaaa agaaccagta 2820 catggggtat attatgaccc atcaaaagac ttgatagctg aaatacagaa acaagggcat 2880 gaccaatgga catatcaaat ttaccaggaa ccattcaaaa atctgaaaac agggaagtat 2940 gcaaaaatga ggacagccca cactaatgat gtaaaacagt taacagaggc agtgcaaaaa 3000 atagccctgg agagcatagt aatatgggga aagattccta aatttagact acccatccaa 3060 aaagaaacat gggaaacatg gtggacagac tattggcaag ccacctggat tcctgagtgg 3120 gagtttgtta atacccctct cttagtaaaa ttatggtacc agctggagaa agaacccata 3180 gtaggagcag aaaccttcta tgtagatgga gcagccaata gggaaactaa attaggaaaa 3240 gcagggtata ttactgacag aggaaggcaa aaaattgtta ctctaactga aacaacaaat 3300 cagaagactg aattacaagc aatttaccta gctttgcaag attcaggatc agaagtaaac 3360 atagtaactg actcacagta tgcgttagga atcattcaag cacatccaga taagagtgaa 3420 tcagagttag tcaaccaaat aatagaacaa ttaataaaga aggaaagggt ctacctgtca 3480 tgggtaccag cacataaagg aattggaggt aatgaacagg tagataaatt agtaagcaag 3540 ggaatcagga aagtgctgtt tctagatgga atagacaagg ctcaagaaga gcatgaaaaa 3600 tatcacaaca attggagagc aatggctagt gaatttaatc taccaccagt agtagcaaaa 3660 gaaatagtag ctagttgtga taaatgtcag caaaaagggg aagccacaca tggacaagta 3720 gactgtagtc cagggatatg gcaattagac tgtacacatt tagaaggaaa aatcatcctg 3780 gtagcagtcc atgtagccag tggctacata gaagcagagg ttatcccagc agaaacagga 3840 caagaaacag catactatat attaaaatta gcaggaagat ggccagtcaa agtaatacat 3900 acagacaatg gtagcaattt taccagtgct gcagttaagg cagcctgttg gtgggcaggt 3960 atcaaacaag aatttggaat tccctacaat ccacaaagtc agggagtagt agaatccatg 4020 aataaagaat taaagaaaat catagggcag gtaagagatc aggctgagca tcttaaaaca 4080 gcagtacaaa tggcagtatt cattcacaat tttaaaagaa aaagggggat tggggggtac 4140 agtgcagggg aaagaataat agacataata gcaacagaca tacaaaccaa agaactacaa 4200 aaacaaatta taaacattca aaaatttcgg gtttattaca gagacagcag agaccccatt 4260 tggaaaggac cagccaaact actctggaaa ggtgaagggg cagtagtaat acaagataat 4320 agtgacataa aagtggtacc aaggaggaaa gcaaaaatca ttagggacta tggaaaacag 4380 atggcaggcg ctgattgtgt ggcaggtaga caggatgagg attagaacat ggaatagttt 4440 agtaaagcac catatgtata tttcacggaa agctaatgga tggttttaca gacatcatta 4500 tgaaagcaga catccaaggg taagttcaga agtacatatc ccattagggg atgctaaatt 4560 agtaataaaa acatattggg gtttgcaaac aggagaaaga gattggcatt tgggtcatgg 4620 agtctccata gaatggagat tgagaagata tagcacacaa gtagaccctg gcctggcaga 4680 ccagctaatt catatgcact attttgattg ttttgcagac tctgccataa gaaaagccat 4740 attaggacac atagttattc ctaggtgtga ctatcaagca ggacataata aggtaggatc 4800 tctgcaatac ttggcactga cagcattgat aaaaccaaaa aagagaaagc cacctctgcc 4860 tagtgttagg aaattagtag aggatagatg gaacaattcc cagaagacca agggccgcag 4920 agggaaccat acagtgagtg gacactagag attctagagg aactcaagca ggaagctgtc 4980 agacactttc ctagaccatg gctccatagc ttaggacaac atatctatga aacttatggg 5040 gatacttgga ctggagtcga ggctataata agaatactgc aacaactact gtttattcat 5100 ttcagaattg ggtgccagca cagcagaata ggcatggttc gacagagaag agcgagaaat 5160 ggagccagta gatcctagca tagagccctg gaaccatcca ggaagtcagc ctaaaactgc 5220 ttgtaataag tgttattgca aacgctgtag ctatcattgt ctagtttgct ttcagacaaa 5280 aggcttaggc atttcatatg gcaggaagaa gcggagacag cgacgcagca ctcctcctag 5340 cagcgaggac catcaagatc ctatatcaaa gcagtaagta tatgtaatgt tagatttact 5400 agcaagagta aattatagag taggagtagg agcattgata gtagcactac tcatagcaat 5460 agttgtgtgg accatagcat atatagaata taggaagctg ttaagacaaa gaaaaataga 5520 ctggttaatt aaaagaatta gggaaagagc agaagacagt ggcaatgaga gtgagggaga 5580 tactgaggaa ttggcaacga tggtggacat ggggcatctt aggcttttgg atgttaatga 5640 tttgtaatgt gtgggggaac ttgtgggtca cagtctatta tggggtacct gtgtggaaag 5700 aagcaaaaac tactctattc tgtgcatcag atgctaaatc atatgagaaa gaagtgcata 5760 atgtctgggc tacacatgcc tgtgtaccca cagaccccaa cccacaagaa atagttttgg 5820 gaaatgtaac agaaaatttt aacatgtgga aaaatgacat ggtggatcag atgcatgagg 5880 atataatcag tttatgggat caaagcctaa agccatgtgt aaagttgacc ccactctgtg 5940 tcactttaaa ttgtacagag gttaatgtta ccagaaatgt taataatagc gtggttaata 6000 ataccacaaa tgttaataat agcatgaatg gagacatgaa aaattgctct ttcaacataa 6060 ccacagaact aaaagataag aaaaagaatg tgtatgcact tttttataaa cttgatatag 6120 tatcacttaa tgagactgac gactctgaga ctggcaactc tagtaaatat tatagattaa 6180 taaattgtaa tacctcagcc ctaacacaag cctgtccaaa ggtctctttt gacccaattc 6240 ctatacatta ttgtgctcca gctggttatg cgattctaaa gtgtaataat aagacattca 6300 atgggacagg accatgccat aatgtcagca cagtacaatg tacacatgga attaagccag 6360 tggtatcaac tcaactactg ttaaatggta gcctagcaga agaagggata ataattagat 6420 ctgaaaatct gacaaacaat gtcaaaacaa taatagtaca tcttaataga tctatagaaa 6480 ttgtgtgtgt aagacccaac aataatacaa gacaaagtat aagaatagga ccaggacaaa 6540 cattctatgc aacaggagac ataataggag acataagaca agcacattgt aacattagta 6600 ggactaactg gactaagact ttacgagagg taaggaacaa attaagagaa cacttcccta 6660 ataaaaacat aacatttaaa ccatcctcag gaggggacct agaaattaca acacatagct 6720 ttaattgtag aggagaattt ttctattgca atacatcggg cctgtttagt ataaattata 6780 cagaaaataa tacagatggt acacccatca cactcccatg cagaataaga caaattataa 6840 atatgtggca ggaagtagga cgagcaatgt acgcccctcc cattgaagga aacatagcat 6900 gtaaatcaga tatcacaggg ctactattgg ttcgggatgg aggaagcaca aatgatagca 6960 caaataataa cacagagata ttcagacctg caggaggaga tatgagggac aattggagga 7020 gtgaattgta taagtataaa gtggtagaaa ttaagccatt gggaatagca cccactgagg 7080 caaaaaggag agtggtggag agagaaaaaa gagcagtggg aataggagct gtgttccttg 7140 ggttcttggg agcagcagga agcactatgg gcgcagcgtc aataacgctg acggcacagg 7200 ccagacaagt gttgtctggt atagtgcaac agcaaagcaa tttgctgagg gctatagagg 7260 cgcaacagca tctgttgcaa ctcacggtct ggggcattaa gcagctccag acaagagtcc 7320 tggctataga aagataccta aaggatcaac agctcctagg actttggggc tgctctggaa 7380 aactcatctg caccactgct gtgccttgga acatcagttg gagtaataaa tctaaaacag 7440 atatttggga taacatgacc tggatgcagt gggatagaga aattagtaat tacacaaaca 7500 caatatacag gttgcttgag gactcgcaga gccagcagga gcaaaatgaa aaagatttat 7560 tagcattgga cagttggaac aatctgtgga attggtttga cataacaaaa tggctgtggt 7620 atataaaaat atttataatg atagtaggag gcttaatagg tttgagaata atttttgctg 7680 tactctctat agtgaataga gttaggcagg gatactcacc tttgtcgttt cagaccctta 7740 tcccgaaccc aagggaaccc gacaggccag gaagaatcga agaagaaggt ggagagcaag 7800 acaaagagag atccgtgcga ttagtgagcg gattcttagc acttgcctgg gacgacctac 7860 ggagcctgtg cctcttcagc taccaccgat tgagagactt catattggtg acagcgagag 7920 cggtggagct tctgagacgc agcagtctca agggactaca gagggggtgg gaagccctta 7980 agtatctggg aagtcttgtg cagtattggg gtctggagct aaaaaagagt gctattagtc 8040 tacttgatac catagcaata gcagtagctg aaggaacaga taggattata gaattaatac 8100 aaggaatttg tagagctatc cgcaacgtac ctagaagaat aagacagggc tttgaaacag 8160 ctttgctata aaatgggggg caagtggtca aaaagcagta tagttggatg gcctgctgta 8220 agagagagaa taagaagaac tgagccagca gcagagggag taggagcagc gtctcaagac 8280 ttagataaat atggagcact tacaagcagc aacacaagta ccactaatgc tgcttgtgcc 8340 tggctggaag cacaagagga ggaagaagtt ggctttccag tcagacctca ggtgccttta 8400 agaccaatga cttataaggc agcagtcgat ctcagcttct ttttaaaaga aaagggggga 8460 ctggaagggt taatttactc taagaaaagg caagaaatcc ttgatttgtg ggtctatcac 8520 acacaaggct tcttccctga ctggcaaaac tacacaccgg gaccaggggt cagatatcca 8580 ctgacctttg gatggtgctt caagctagtg ccagttgatc caggggaagt agaagaggcc 8640 aacgaaggag aaaacaactg tctgctacac cctatgagcc agcaaggaat ggatgatgat 8700 cacagagaag tattaaagtg gaagtttgac agtcacctag cacataaaca catggcccga 8760 gagctacatc cggagtatta caaagactgc tgacacagaa gggactttcc gctgggactt 8820 tccactgggg ttccaggagg tgtggtctgg gcgggactgg ggagtggtca accctcagat 8880 gctgcatata agcagctgct tttcgcttgt actgggtctc tctaggtaga ccagatctga 8940 gcctgggagc tctctggcta tctagggaac ccactgctta agcctcaata aagcttgcct 9000 tgagtgctct 9010 9 8972 DNA Human immunodeficiency virus type 1 isolate=96ZM751.3; 137.1632gag; 1419.4435pol; 4380.4958vif; 4898.5188vpr; 5169.7814tat; 5308.7938rev; 5407.5667vpu; 5585.8128env; 8130.8753nef 9 ccgaaagcga aagtaagacc agaggagatc tctcgacgca ggactcggct tgctgaagtg 60 cactcggcaa gaggcgagag cggcggctgg tgagtacgcc aattttattt gactagcgga 120 ggctagaagg agagagatgg gtgcgagagc gtcaatatta agaggcggaa aattagatga 180 atgggaaaga attaggttaa ggccaggggg aaaaaagcac tatatgatga aacacttaat 240 atgggcaagc agggagctgg aaagatttgc acttaaccct ggccttttag agacatcaga 300 aggctgtaaa caaataatac aacagctaca accagctctc cagacaggaa cagaggaact 360 taggtcatta tataatacag tagcaactct ctattgtgta catgaaaaga taaaggtacg 420 agacaccaag gaagccctag acaagataga ggaagaacaa aacaaaagtc aacaaaaaat 480 acaaaaaaca gaagcgactg gcggaaaggt cagtcaaaat tatcctatag tgcagaatct 540 ccaagggcaa atggtacacc aggctatatc acctagaact ttgaatgcat gggtaaaagt 600 aatagaggag aagggtttca acccagaggt aatacccatg tttacagcat tatcagaagg 660 agccacccca caagatctaa acaccatgtt aaatacagtg gggggacatc aagcagccat 720 gcaaatgtta aaagatacca tcaatgagga agctgcagaa tgggataggt tacatccagt 780 acatgcaggg cctattgcac caggccaaat aagagaacca aggggaagtg acatagcagg 840 aactactggt acccttcagg aacaaatagc atggatgaca aataacccac ctattccagt 900 gggagacatc tataaaagat ggataattct ggggttaaat aaaatagtaa gaatgtacag 960 ccctgtcagc attctggaca taaaacaagg accaaaggaa ccctttaggg actatgtaga 1020 tcggttcttt aaaactttaa gagctgaaca agctacacaa gatgtaaaaa ttggatgaca 1080 gacaccttgt tggttcaaaa tgcgaaccca gattgtaaga ccattttaag ggcattagga 1140 ccaggggcta cattagaaga aatgatgaca gcatgtcagg gagtgggggg acctggccac 1200 aaagcaagag ttttggctga agcaatgagc caagtaaaca atacaaacat aatgatgcag 1260 aaaagcaatt ttaaaggccc taaaagaatt gttaaatgtt tcaactgtgg cagggaaggg 1320 catatagcca ggaattgcag ggctcctggg aaaaaaggct gttggaaatg tggaaaggaa 1380 ggacaccaaa tgaaagactg tactgagaga caggctaatt ttttagggaa aatttggcct 1440 tcccagaagg ggaggccggg gaacttcctt cagaacagac cagagccaac agccccacca 1500 gctccaacag ccccaccagc agagagcttc aggttcgagg agacaacccc tgccccgagg 1560 caggagcaga aagacaagga acccttaact gccctcaaat cactctttgg cagcgacccc 1620 ttgtctcaat aaaagtaggg ggtcagataa aggaggctct cttggataca ggagcagatg 1680 atacagtatt agaagaaata aatttgccag gaaaatggaa accaaaaatg ataggaggaa 1740 ttggaggttt tatcaaagta agacagtatg atcaaatact tatagaaatt tgtggaaaaa 1800 aggctatagg tacagtatta gtaggaccta cacctgtcaa cataattggg agaaatatgt 1860 tgacccagct tggctgcaca ctaaattttc caattagtcc tattgaaact gtaccagtaa 1920 aattaaagcc aggaatggat ggcccaaggg tcaaacaatg gccattgaca gaagaaaaaa 1980 taaaagcatt aacagcaatt tgtgaagaaa tggaaaagga aggaaaaatt acaaaaattg 2040 gccctgagaa tccatataac actccagtat ttgccataaa aaagaaggac agtactaagt 2100 ggagaaaatt agtagatttc agggaactca ataaaagaac tcaggacttt tgggaagttc 2160 aattaggaat accacaccca gcggggttaa aaaagaaaaa gtcagtgaca gtactggatg 2220 tgggggatgc gtatttttca gttcctttag atgaaggctt caggaaatat actgcattca 2280 ccatacctag tataaacaat gaaacacctg ggattagata tcaatataat gtgcttccac 2340 agggatggaa aggatcacca tcaatattcc agagtagcat gataaaaatc ttagagccct 2400 ttaggacaca aaacccagaa atagttatct atcaatatat ggatgacttg tatgtaggat 2460 ctgatttaga aatagggcaa cacagagcaa aaatagagga gttaagagaa cacctattga 2520 gatggggatt tactacacca gacaagaagc atcagaaaga gcccccattt ctttggatgg 2580 ggtatgaact ccatcctgac aaatggacag tacagcctat aaagctgcca gaaaaggaga 2640 gctggactgt caatgatata cagaagttag tgggaaaatt aaactggcaa gtcagattta 2700 cgcagggatt aaagtaaggc aactgtgtaa actccttagg ggagccaaag cactaacaga 2760 catagtacca ttgactgaag aggcagaatt agaattggca gagagcaggg aaattctaaa 2820 agaaccagta catggagtat attatgaccc atcaaaagac ttaatagctg aaatacagaa 2880 acaagggcat gaccaatgga catatcaagt ttaccaagaa ccattcaaaa atctgaaaac 2940 aggaaagtat gcaaaaatga ggactgccca cactaatgat gtaaaacagt taacagaggc 3000 ggtgcaaaaa atagccatgg aaagcatagt aatatgggga aagattccta aatttaggct 3060 acccattcaa aaagaaacat gggagacatg gtggacagac tattggcaag ccacctggat 3120 tcctgagtgg gagtttgtta atactccccc cctagtaaaa ttatggtacc agctggagaa 3180 agaacccata gcaggagcag aaacttacta tgtagatgga gcagccaata gggaaactaa 3240 aataggaaaa gcagggtatg ttactgacag aggaaggcaa aaaattgtta ctctaactga 3300 aacaacaaat caaaagactg aattacaagc aattcagtta gctttgcagg attcaggatc 3360 agaagtaaac atagtaacag actcacagta tgcattagga atcatccaag cacaaccaga 3420 taagagtgaa tcagaattag tcaatcaaat aatagaacag ttgataaaaa aggaaagggt 3480 ttacctgtca tgggtaccag cacacaaagg aattggagga aatgaacaag tagataaatt 3540 ggtaagtagt ggaatcagga aagtgctgtt tctagatgga atagataagg ctcaagaaga 3600 gcatgaaaaa tatcacagca attggagagc aatggctagt gagtttaatc tgccacccat 3660 agtagcaaaa gaaatagtag ccagctgtga taaatgtcag ctaaaagggg aagccataca 3720 tggacaagta gactgtagtc caggaatatg gcaattagat tgtacccatt tagaaggaaa 3780 agtcatcttg gtagcagtcc atgtagccag tggttacata gaagcagagg tcaccccagc 3840 ggaaacagga caagaaacag cacttttcat actaaaatta gcaggaagat ggccagtcaa 3900 agtagtacat acagacaatg gcagtaattt caccagtgct gcagtcaagg cagcctgttg 3960 gtgggcaggt atccaccagg aatttggaat tccctacaat ccccaaagtc aaggagtagt 4020 agaatccatg aataaagaat taaagaaaat tatagggcag gtaagagatc aagctgagca 4080 ccttaagaca gcagtacaaa tggcagtatt cattcacaat tttaaaagaa aaggggggat 4140 tggggggtac agtgcagggg aaagaataat agacataata gcaacagaca tacaaactag 4200 agaattacaa aaacaaatta taaaaattca aaattttcgg gtttattaca gagacagcag 4260 agaccctatt tggaaaggac cagccaaact actctggaaa ggtgaagggg cagtagtaat 4320 acaagataat agtgacataa aggtaatacc aaggaggaaa gcaaaaatca ttagggacta 4380 tggaaaacag atggcaggta ctgatagtgt ggcaggtaga caggatgaag attagaacat 4440 ggaatagttt agtaaagcac catatgtatg tttcaaaaag aactggtaga tggttttaca 4500 gacatcatta tgaaagcaga catccaaaaa taagttcaga agtacacatc ccattagggg 4560 atgccaaatt agtaataaaa acatattggg ggctgcatcc aggggaaaga gaatggcatt 4620 tgggtcatgg agtctccata gaatggagat tgagaagata cagcacacaa gtagaccctg 4680 gcctggcaga ccagctaatt catatgcatt attttaattg ttttgcagac tctgccataa 4740 gaaaagccct actaggacat atagttattc ctaggtgtga ttatcaagca ggacataata 4800 aggtaggatc cctacaatac ttggcactga cagcattgat aaaaccaaaa aagataaagc 4860 cacctttacc tagtgttagg aaattagtag aggatagatg gaacaagccc cagaaaacca 4920 agggccgcag agggaaccat ataatgaatg ggcactagag cttttagagg agctcaagca 4980 ggaagctgtc agacactttc ctagaacatg gctccataac ttaggacaac atatctacca 5040 aacctacggg gatacttgga cgggggttga agctctaata agaatactgc aacaactact 5100 gtttattcat ttcagaattg gatgccaaca tagcagaata ggcattatgc gacagagaag 5160 agcaagaaat ggagccagta gatcctagac tagagccctg gaatcatcca ggaagtcaac 5220 ctaaaactcc ttgtaataag tgttattgta aacactgtag ctatcattgt ctagtttgct 5280 ttcagacaaa aggcttaggc atttcctatg gcaggaagaa gcggagacaa cgacgaagcg 5340 ctcctccaag cagtgaggat catcaaaatc ctatatcaaa gcagtaagta caaagtaata 5400 gatgtaatgt taaatttaga agcaagagta gattatagaa taggagtagg agcattaata 5460 gcagcactaa tcatagcaat agctgtgtgg atcatagtat atatagaata tagaaaattg 5520 tcaagacaaa gaaaaataga ccggttaatt aaaagaatta gagaaagggc agaagacagt 5580 ggcaatgaga gtgaagggga taatgaggaa ttggcaacaa tggtggatat ggggcatctt 5640 aggcttttgg atgctattga tgtgtaatgc aatggggaaa ttgtgggtca cagtctacta 5700 tggggtacct gtgtggaaag aagcaaaaac tactttattt tgtgcatcag atgctaaagc 5760 atatgagaca gaagtgcata atgtttgggc tacacatgcc tgtgtaccca cagaccccaa 5820 cccacaagaa atggttttgg aaaatgtaac agaaaagttt aacatgtggg aaaataacat 5880 ggtggatcag atgcatgagg atataatcag tttatgggac caaagcctaa agccatgtgt 5940 aaagttgacc ccactctgtg tcactttaaa ctgtactgct aatataacca acaatgctaa 6000 tataaccaac aatgctaata taaccaacta taataatgaa actgacatga gaaattgctc 6060 tttcaatata accacagaat taagagataa gaggaggcaa gtagatgcac tcttttataa 6120 acttgatata gtaccaatta atgagaattc cagtgaatat agattaataa attgtaatac 6180 ctcggccata acacaagcat gtccaaaggt tacttttgac ccaatcccta tacattattg 6240 tgctccagct ggttatgcga ttctaaagtg taacaataag acattcaatg gaacaggacc 6300 atgcaataat gtcagcacag tacaatgtac acatggaatt aagccagtag tatcaactca 6360 attactgtta aatggtagtc tagcagaaga agagataata attagatcta aaaatatgac 6420 agacaatgcc aaaataataa tagtacatct taatgaatct gtagaaattg tgtgtacaag 6480 acccaacaat aatacaagga aaagtgtgag gataggacca ggacaaacat tctatgcaac 6540 aggagaaata ataggaaata taagacaagc atattgtaac atcagtgaag gcaaatggaa 6600 taacactcta caaagggtag gtgaaaaatt aagaaaatac ttccctaata aaacaataag 6660 ctttgcacca tcctcaggag gggacctaga aattacaaca catagcttta attgtagagg 6720 agaatttttc tattgcaata catcaaaact gtttaatggt acgtttaatg gtacaaacac 6780 ttctaatgat agaagtaatt cgaccattac gcttcaatgc agaataaaac aaattacaaa 6840 catgtggcag ggggtaggac aagcaatgta tgctcctcca attaaaggaa acataacatg 6900 taaatcaaat atcacaggac tactattaac acgtgatgga gggacaaatg acacagagac 6960 accagagaca ttcagacctg gaggaggaga catgaaggac aattggagaa gtgaattata 7020 taaatataaa gtggtagaaa ttaagccatt aggagtagca cccactaagg cacgaaggag 7080 agtggtggag agagaaaaaa gagcagtagg aataggagct gtgttccttg ggttcttggg 7140 agcagcagga agcactatgg gcgcagcatc aataacgctg acggtacagg tcagacaatt 7200 attgtctggt atagtgcaac agcaaagcaa tttgctgagg gctatagagg cgcaacagca 7260 catgttgcaa ctcacagtct ggggcattaa gcagctccag gcaagagtct tggctataga 7320 aagataccta aaggatcaac agctcctagg gatttggggc tgctctggaa aactcatctg 7380 caccactgct gtgccttgga actctagttg gagcaacaaa tctgaacggg agatttggga 7440 taacatgacc tggatgcagt gggatagaga aattaataat tacacagaaa caatatatag 7500 gttgcttgaa gtctcgcaaa accagcagga aaataatgaa agggatttac tagcattgga 7560 cagttgaaaa aatctgtgga attggtttaa tataacaaat tggctgtggt atataaaaat 7620 attcataatg ataataggag gcttgatagg tttaagaata atttttgctg tgctctctat 7680 agtaaataga gttaggcagg ggtactcacc tttgtcgttg cagaccctta tcccaacccc 7740 gagggaacca gacaggctcg gaagaatcga agaagaaggt ggagagcaag acagagacag 7800 atcaattcga ttagtgaacg gattcttagc acttgtctgg gacgacctcc ggagcctgtg 7860 ccttttcagc taccaccgct tgagagactt catattgatt gcagcgaggg gactacagag 7920 ggggtgggaa actcttaagt atctggggag tcttgtacag tattggggtc tagagctaaa 7980 aaagagtgct attagtttgc ttgatactat agcaatagca gtagctgaag gaacagatag 8040 aattatagaa ttaacacaaa gaatttgtag agctatccgc aacgtaccta gaagaataag 8100 acagggcttt gaagcagctt tgcaataaga tgggaggcaa gtggtcaaaa cgcagtatag 8160 ttggatggcc taaagtaaga gaaagaatag caagaactga tccagcagca gagggagtag 8220 gagcagcgtc tcaagactta gataaatatg gggcacttac aagcagtaac acaagtacca 8280 ataatgctga ttgtgcctgg ctggaagcgc aagaggagga gggagaagta ggctttccag 8340 tcagacctca ggtaccttta agaccaatga cttataagtc agcatttgat ctcagcttct 8400 ttttaaaaga aaagggggga ctggatgggt taatttactg taagaaaaga caagaaatcc 8460 tcgatttgtg ggtctatcac acacaaggct acttccctga ttggcaaaac tatacaccgg 8520 gaccagggat cagatatcca ctgacctttg gatggtgcta caagctagtg ccagttgacc 8580 caagggaagt agaagaagcc aacgaaggag aggacaactg tttgctacac cctataagcc 8640 agcatggaat agaagatgaa gacagagaag tattaaggtg gaagtttgac agttccctag 8700 cacgcagaca catggcccgc gagctacatc cggagtatta caaagactgc tgacacagaa 8760 gggactttcc gctgggactt tccactgggg cgttccaggg ggtgtgatct gggcgggact 8820 ggggagtggc cagccctcag aagctgcata taagcagctg cttttcgcct gtactgggtc 8880 tctctaggta gaccagatct gagcccggga gctctctggc tatctaggga acccactgct 8940 taagcctcaa taaagcttgc cttgagtgcc tt 8972 10 9060 DNA Human immunodeficiency virus type 1 isolate=94CY017.41; 159.1649“gag”; 1442.4453“pol”; 4398.4976“vif”; 4916.5206“vpr”; 5187.7841 “tat”; 5326.8046“rev”; 5428.5673“vpu”; 5591.8188“env”; 8190.8843“nef” 10 ttgaaaagcg aaagtaacag ggactcgaaa gcgaaagttc cagaggagtt ctctcgacgc 60 aggactcggc ttgctgaggt gcacacggca agaggcgagg ggcggcgact ggtgagtacg 120 cctaatattt ttgactagca gaggctagaa ggagagagat gggtgcgaga gcgtcaatat 180 taagcggggg aaaattagat gcttgggaga aaattcggtt aaggccaggg ggaaagaaaa 240 aatatagact gaaacatttg gtatgggcaa gcagggagct ggagaaattc tcaattaacc 300 ctggcctttt agaaacacca gagggatgta gacaaataat aaggcagtta caaccagctc 360 tccaaacagg aacagaagaa cttaaatcat tatataatac agtagtagtc ctctactggg 420 tacatcaaag ggtagatgta aaagacacca aggaagctct agataaaata gaggaagaac 480 aaaacaagca gaaaacacag catgcagcag ctgacacagg gaacagcagc agtcaaaatt 540 atcccatagt gcaaaatgca caagggcaaa tggtacacca ggctatatca cctaggacgt 600 tgaatgcctg ggtcaaagta gtagaagaaa aggctttcag cccagaagta atacctatgt 660 ttacagcatt atcagaagga gccaccccac aagacttaaa tactatgcta aacacagtgg 720 ggggacatca agcagctatg caaatgttaa aagataccat caatgaggaa gctgcagaat 780 gggacagggt acatccagta catgcagggc ctattccacc aggccagatg agagaaccaa 840 ggggaagtga catagcagga actactagta cccttcagga acaaataggt tggatgacca 900 gcgatccacc catcccagtg ggagaaattt ataaaagatg gataatcctg ggattaaata 960 aaatagtaag aatgtatagc cctgtcagca ttttggacat aagacaaggg ccaaaagaac 1020 cctttagaga ttatgtggat aggttcttta aaactctaag agctgagcaa gccacacagg 1080 aggtaaaaaa ctggatgacg gacaccttgc tggtccaaaa tgcgaaccca gattgtagat 1140 ccatcttgag agcattagga ccaggggcct cattagaaga aatgatgaca gcatgtcagg 1200 gagtgggagg acccagccat aaagcaaggg ttttggctga agcaatgagc catgtacaaa 1260 gtacaaatac aaacataatg atgcagagag gcaattttag gggtcaaaaa agaattaagt 1320 gtttcaactg tggcaaggaa ggacacctag ccagaaattg cagggcccct aggaaaaagg 1380 gctgctggaa atgtggaaag gaaggacatc aaatgaaaga ttgcactgag agacaggcta 1440 attttttagg gaaaatttgg ccttccaaca aagggaggcc aggaaatttt cctcagagca 1500 gaacagagcc aacagcccca ccagcagaga acttgagaat gggggaagag ataacctcct 1560 ccctgaagca ggaactggag accagggaac catacaatcc tgcaatttcc ctcaaatcac 1620 tctttggcaa cgaccccttg ttacagtaaa gatagaggga cagctaaaag aagctctatt 1680 agatacagga gcagatgata cagtgttaga agaaataaat ttgccaggaa aatggaaacc 1740 aaaaatgata gggggaattg gaggttttat caaagtaaga caatatgatc agatagctat 1800 agaaatttgt ggaaaaaggg ccataggtac agtattagta ggacctaccc ctgtcaacat 1860 aatcggaaga aatatgttgg ttcagcttgg ttgtacttta aattttccaa ttagtcctat 1920 tgaaactgta ccagtaaaat taaagccagg aatggatggt ccaaaggtta aacaatggcc 1980 attgacagaa gaaaaaataa aagcattaac agaaatctgt aaagaaatgg aaaaggaagg 2040 aaaaatttca aaaattgggc ctgaaaatcc atacaacact ccagtgtttg ctataaagaa 2100 aaaagacagc actaaatgga gaaaattagt agattttaga gaactcaata agagaactca 2160 agacttctgg gaagttcagt taggaatacc acatccagca ggattaaaaa agaaaaaagc 2220 agtaacagta cttgatgtgg gggacgcata tttttccgtt cccttacatg aagacttcag 2280 aaaatatact gcattcacca tacctagtac caacaatgag acaccaggag ttaggtatca 2340 gtacaatgta cttccacagg gatggaaagg atcaccagca atattccaga gtagcatgac 2400 aaagatctta gagcccttta gatcaaagaa tacagaatta atcatctacc aatacatgga 2460 tgacttgtat gtaggatctg atttagaaat aagccagcat agagtaaaaa tagaggaatt 2520 aagggctcac ttattgaaat ggggatttta tacaccagac aaaaaacatc agaaagaacc 2580 tccatttctt tggatgggat atgagcttca tcctgacaaa tggacagtcc agcctataaa 2640 gctgccagaa aaagacagct ggactgtcaa tgatatacag aaattagtag ggaaattaaa 2700 ttgggcaagt cagatttatg cagggattaa agtaaagcaa ctgtgtaaac tccttagagg 2760 agccaaagca ctaacagaca tagtaacact gactaaagaa gcagagttag aattagaaga 2820 gaacagggaa attttaaaaa cccctgtaca tggggtatac tatgacccat caaaagactt 2880 aatagcagaa atacagaaac aagggcaaga ccaatggaca tatcaaattt atcaggaacc 2940 ctttaagaat ctgaaaacag ggaaatatgc aaaaaggagg tccacccaca ctaatgatat 3000 aaaacagtta acagaagcag tacaaaaaat aaccatggaa agcatagtga tatggggaaa 3060 gactcctaaa tttaaattac ccatacaaaa ggaaacatgg gagacatggt gggcggagta 3120 ttggcaggct acctggattc ctgagtggga gtttgtcaat acccctcctc tagtaaaact 3180 gtggtaccag ttagaaaaag aacccatagc aggagcagaa actttctatg tagatggggc 3240 agctaataga gagactaaac taggaaaggc agggtatgtc actgacagag gaagacaaaa 3300 aattgtctcc ctgacggaga caacaaatca aaagactgaa ttacatgcaa tctatttggc 3360 tttacaggat tcaggattag aagtgaacat agtgacagat tcacagtatg cattaggaat 3420 cattcaagca caaccagaaa ggagtgaatc agagatagtc aatcaaataa tagaaaaatt 3480 aatagaaaag gaaagggtct acctatcatg ggtaccagca cacaaaggga ttggaggaaa 3540 tgaacaagta gacaaattag tcagttctgg aatcaggaaa gtgctatttt tagatgggat 3600 agataaggct caagaggaac atgaaagata tcacagcaat tggagagcaa tggctcatga 3660 ctttaatcta ccacctgtag tagcaaaaga aatagtagct agctgtgata aatgtcagct 3720 aaaaggggaa gccatgcatg gacaagtaga ctgtagtcca ggaatatggc aactagattg 3780 cacacatctt gaaggaaaag ttatcctggt ggcagtccat gtggccagtg gctatataga 3840 agcagaagtc atcccaacag aaacaggaca ggatacagca tactttatat taaaactagc 3900 aggaagatgg ccagtaaaag taatacatac agacaatggg cccaatttca tcagtgcaac 3960 agttaaggca gcctgttggt gggcaggtat ccaacaagaa tttgggattc cctacaatcc 4020 ccaaagtcaa ggagtagtgg aatctatgaa taaagaatta aagaaaatca tagggcaggt 4080 aagagatcaa gctgaacacc ttaagacagc agtacaaatg gcagtattca ttcacaattt 4140 taaaagaaaa ggggggattg ggggatacag tgcaggggaa agaataatag acataatagc 4200 aacagatata caaactaaag aactacaaag acaaattaca aaaattcaaa attttcgggt 4260 ttattacagg gacagcagag atccaatttg gaaaggacca gcaaaactcc tttggaaagg 4320 tgaaggggca gtagtaatac aagacaatag tgacataaag gtagtaccaa gaagaaaagc 4380 aaagatcatt agggattatg gaaaacagat ggcaggtgat gattgtgtgg caggtagaca 4440 ggatgaggat tagaacatgg aacagtttag ttaaacatca tatgtatatt tcaaggaaag 4500 ctaaaggttg ggtctataaa catcactatg aaagcagaaa tccaagaata agttcagaag 4560 tacacatccc gctaggggag gctagaataa tagtaagaac atattggggt ctgcacatag 4620 gagaaaaaga ctggcacttg ggtcatggag tctccataga atggaggcaa aacaggtatc 4680 atacacaaat agaccctgat ctggcagacc atctaatcca tctgtattat tttgactgtt 4740 tttcagaatc tgccataagg aaagccataa taggagaaat agttagtcct aggtgtgaat 4800 atcaagcagg acataacaag gtagggtctc tgcaatattt ggcattgaaa gcagtagtag 4860 cttcaacaag gacaaagcca cctttgccta gtgttaggaa attagtagag gatagatgga 4920 acaagcccca gaagaccaag ggccacagag ggagccatac aatgaatgga tgttagaact 4980 gttagaggag ctcaagcagg aagctgttag acatttccct aggcactggc tacatggcct 5040 aggacaatac atctataata cctatgggga tacctgggaa ggagttgaag ttatcataag 5100 atatctgcaa caactactgt ttgtccattt cagaattggg tgccaacata gcaggatagg 5160 cattattcga agaagaagag taagggatgg agccagtaga ccctaaacta gagccctgga 5220 accatccggg aagtcagcct aaaactgctt gtaccaaatg ttattgtaaa cgctgttgct 5280 atcattgcca gttgtgcttt ataaacaaag gcttaggcat ctcctacggc aggaagaagc 5340 gacgaccccg acgaaagcct tctccaagca ataaggacca tcaaaatcct ataccaaagc 5400 agtaagtagt agtaattaat atatgtaatg ttacctttag taatattggc aatagtagga 5460 ctgatagtag ctttaatctt agcaatagtt gtatggacta tagtattcat agaatataag 5520 aaaattaaga agcaaaggaa aatagactgg ttaatcaaaa gaataagtga gagagcagaa 5580 gacagtggca atgagagtga tggggacaca gaggaactat cagcacttgt ggagaggggg 5640 catcttgatt ttggggatgt taataatgtg taaagctaca gatttgtggg tcacagtata 5700 ctatggagta cctgtgtgga aagatgcaga taccatccta ttttgtgcat cagatgctaa 5760 agcatatgat acagaagtgc ataatgtatg ggccacacat gcctgtgtac ccacagaccc 5820 caacccacaa gaaataaacc tggaaaatgt aacagaaaat tttaatatgt ggaaaaataa 5880 catggtagag cagatgcaag aagatataat cagcttatgg gatcaaagcc taaagccatg 5940 tgtaaaatta accccgctct gcgtcatttt aaattgtagc aatgccaata ccagcaccca 6000 tagcaatagc agtagcaccc agagccccat taatgaagaa ataaaaaact gctcttacaa 6060 tactaccaca atactaagag ataagacaca aaaagtttat tcactgtttt atagacttga 6120 tgtagtacaa cttgatgaaa gtgaaaataa gaatacatca ggtagtaata ctctgtatag 6180 actaataaat tgtaatacct caaccatcac acaagcgtgt ccaaaggtaa cctttgagcc 6240 aattcctata cattattgtg ccccagctgg ttttgcgatt ctaaagtgta aggatccgag 6300 attcaatgga acagggtcat gcaagaatgt tagctcagta caatgtacac atggaattaa 6360 accagtagca tcaactcaac tgctgttgaa tggcagtcta gcagaaggag ggaaaataat 6420 gattagatct gaaaatatta caaacaatgc caaaaacata atagttcagt ttactaagcc 6480 tgtactaatt acttgtatca gacccaacaa caatacaaga aaaagtatac gctttggacc 6540 aggacaagcc ttctatacaa atgaaataat aggggacata agacaagcac attgtaatat 6600 caacaaaaca ttatggaatg acactttaca aaaggtagct gaacaattaa gagagaaatt 6660 ccctaagaaa accataatct ttactaactc ctcaggaggg gacccagaaa ttacaacact 6720 tagttttaat tgtgcaggag aatttttcta ttgcaataca acaggcctgt ttaatggtac 6780 gtggtggaac aatggtacgt ggaacgggcc ctacacacct aataacacca atggaagtat 6840 aatcctccca tgcagaataa aacaaattat aaacatgtgg cagagagtag gaagagcaat 6900 gtatgcccct cccattgcag gaataataaa gtgtacatca aacattacag gaataatatt 6960 gacaagagat ggtggtaaca atgggactaa tgagaccttc agacctggag gaggagatat 7020 gagggacaat tggagaagtg aattatataa atataaagta gtaaaacttg aaccactagg 7080 agtagcacct accagggcaa aaagaagagt ggtggagaga gaaaaaagag cagttggact 7140 gggagctgtc ttccttgggt tcttgggagc agcaggaagc actatgggcg cggcgtcact 7200 aacgctgacg gtacaggcca gacaattatt gtctggtata gtgcaacagc aaagcaattt 7260 gctgcaggct atagaagctc aacagcatct gttgaaactc acagtctggg gcattaaaca 7320 gctccaggcg agggtcctgg ctgtggaaag atacctaaag gatcaacagc tcctgggaat 7380 ttggggctgc tctggaaaac tcatctgcgc cactactgtg ccctggaaca ctagttggag 7440 taataagtct caggatgaga tttgggacaa catgacctgg ttgcaatggg ataaagaaat 7500 tagcaattac acaaacataa tatataggtt acttgaagaa tcgcaaaacc agcaggaaaa 7560 gaatgagcaa gacttattgg cattagacaa atgggcagat ttgtggagtt ggttcaacat 7620 ttcacactgg ctgtggtata taagaatatt tataatgata gtaggaggct tgataggatt 7680 aagaatagtt tttgctataa ttactgtagt aaatagagtt aggcagggat actcacctgt 7740 gtcatttcag atccctaccc caagcccaga gggtcccgac aggcccagag gaaccgaaga 7800 aggaggtgga gagcaaggca gagacagatc gattcgatta gtgaacgggt tcttcgcact 7860 tgcctgggac gacctacgga gcctgtgcct cttcagttac caccgcttga gagattgcat 7920 attgattgca gcgaggactg tggaacttct gggacactgc agtctcaagg gactgagact 7980 ggggtgggaa ggtctcaaga atctgtggaa tcttctgtta tactggggtc gggaactgaa 8040 gaatagtgct attagcttat ttgatactat agcagtagca gtagctgagt ggacagatag 8100 ggttatagaa atagggcaaa gagctttcag agctattctc aacataccta gaagaatcag 8160 acagggctta gaaagggctt tactataaaa tggggggcaa gtggtcaaaa aggagcatac 8220 caggatggcc tgctattagg gagagaatga gaagaactcc tccaacagca caaagaacag 8280 aagcagtgtc tccagcagca ccaggagtag gagcagtgtc tcaagattta gctactcatg 8340 gagcagtcac aagcagtaat acagcagcta ctaatcctga ttgcgcctgg gtggaagcgc 8400 aagaagagga gagtgaagta ggcttcccag tcaggccaca ggtaccttta aggccaatga 8460 ccttcaaggg agcgtttgat ctcagcttct ttttaaaaga aaagggggga ctggatgggt 8520 taatttactc ccagaaaaga caagacatcc ttgatatgtg ggtctaccac acacaaggct 8580 acttccctga ttggcagaat tacacaccag ggccagggat cagataccca ttaacatttg 8640 gatggtgctt caagctagta ccagtagagc catctgaggt agaagaagct actcagggag 8700 agaacaacag cttattacac cctatatgcc aacatggagt agatgaccct gaaagagaag 8760 tgttaagatg ggagtttgat agaagcctgg cacggagaca cagagcccga gagctgcatc 8820 cggagtacta caaagactgc tgacacagaa gttgctgacg gggactttcc gctggggact 8880 ttccagggag gtgtggtgtg ggcggagttg gggagtggct aaccctcaga tgctgcatat 8940 aagcagctgc ttctcgcatg tactgggtct ctcttgttgg accagataga gcccgggagc 9000 tctctggcta gcaggggaac ccactgctta agcctcaata aagcttgcct tgagagcttc 9060 11 8959 DNA Human immunodeficiency virus type 1 isolate=94IN476.104; 138.1613“gag”; 1418.4428“pol”; 4361.4939“vif”; 4879.5169“vpr”; 5150.7782tat“; 5289.7939”rev“; 5378.5638”vpu“; 5556.8129”env“; 8131.8754nef 11 ttgaaagcga aagtaagacc agaggagatc tctcgacgca ggactcggct tgctgaagtg 60 cactcagcaa gaggcgaggg gggcgactgg tgagtacgcc aatttttatt tgactagcgg 120 aggctagaag gagagagatg ggtgcgagag cgtcaatatt aagaggggga aaattagata 180 gatgggaaaa aattcggtta aggccagggg gaaagaaaca ttatatgata aaacacttag 240 tatgggcaag cagggagctg gaaagatttg cgcttaaccc tggcctttta gagacgtcag 300 acggatgtaa acaaataata aaacagctac atccagctct taagacagga acagaggaac 360 ttaggtcatt attcaacaca gtagcaactc tctattgtgt acatgcaggg atagaggtac 420 gagacaccaa ggaagcctta gacaagatag aggaagaaca aaacaaaagt cagcaaaaaa 480 tacagcaggc aaaagaggct gacggaaagg tcagtcaaaa ttatcctata gtgcaaaatc 540 tccaagggca aatggtacac cagcccctat cacctagaac tttgaatgcg tgggtaaaag 600 taatagagga gaaggctttt agcccagagg taatacccat gttcacagca ttatcagaag 660 gagccacccc ctctgattta aacaccatgt taaatacagt ggggggacat caagcagcca 720 tgcaaatgtt aaaagatacc atcaacgagg aggctgcgga atgggataga ttacatccag 780 tacatgcagg gcctaatcca ccaggccaga tgagagaacc aaggggaagt gatatagcag 840 gaactactag tacccttcag gaacaaatag catggatgac aggtaaccca cctattccag 900 tgggagacat ctataaaaga tggataattc tggggttaaa taaaatagta agaatgtata 960 gccctgtcag cattttggac ataagacaag ggccaaagga accctttaga gactatgtag 1020 accggttctt taaaacttta agagctgaac aagctacaca agaagtaaaa ggttggatga 1080 cagacacctt gttggtccaa aatgcaaacc cagattgtaa gaccatttta agagcattag 1140 gaccaggggc ttcattagaa gaaatggtga cagcatgtca aggagtggga ggacctagcc 1200 acaaagcaag agtgttggct gaggcaatga gccaatcaca tagtaacata atgatgcaga 1260 gaggcaattt taaaggccct aaaagaattg ttaaatgctt caactgtggc aaggaagggc 1320 acatagccag aaattgcagg gcccctagaa aaagaggctg ttggaaatgt gggcaagaag 1380 gacaccaaat gaaagactgt actgagaggc aggctaattt tttagggaaa atttggcctt 1440 cccacaaggg gaggccaggg aatttccttc aaaacaggcc agagccaaca gccccaccag 1500 cagagagctt caggttcaag gagacaaccc ccgctccgaa gcaggagtcg aaagacaggg 1560 aacccttaac ttccctcaaa tcactctttg gcagcgaccc cttgtctcaa taaaagtagg 1620 gggccagata aaggaagctc tcttagacac aggagcagat gatacagtat tagaagaaat 1680 agctttgcca ggaagatgga aaccaaaaat gataggagga attggaggtt ttatcaaagt 1740 aagacagtat gatcaaatac ttatagaaat ttgtggaaaa aaggctatag gtacagtatt 1800 agtaggacct acacctgtca acataattgg aagagatatg ttgactcagc ttggatgcac 1860 tctaaatttt ccaattagcc ccattgaaac tgtaccagta aaattaaagc caggaatgga 1920 tggcccaaag gttaaacagt ggccattgac agaagagaaa ataaaagcat taacagaaat 1980 ttgtaaagaa atggagaagg aaggaaaaat tacaaaaatt gggcctgaaa atccatataa 2040 cactccagta tttgccataa aaaggaagga cagtactaag tggagaaaat tagtagattt 2100 cagggagctc aataaaagaa ctcaagactt ttgggaagtt caattaggaa taccacaccc 2160 agcaggttta aaaaagaaaa aatcagtgac agtactggat gtgggggatg catatttttc 2220 agttccttta gatgaaggct tcgggaaata tactgcattc accataccta gtataaacaa 2280 tgaaacacca gggattagat atcaatataa tgtgcttcca cagggatgga aaggatcacc 2340 agcaatattc cagagtagca tgacaaaaat cttagagccc tttagggcac gaaatccaaa 2400 aatagtcatc tatcaatata tggatgactt gtatgtaggg tctgacttag aaatagggca 2460 tcatagagca aaaatagagg agttaagagc acatctatta aagtggggat tcaccacacc 2520 agataagaaa catcagaaag aacccccatt tctttggatg gggtatgaac tccatcctga 2580 caaatggaca gtacagccta taaagctgcc agaaaaggat agctggactg tcaatgatat 2640 acagaagtta gtgggaaaat taaactgggc aagtcagatt tacccaggga ttaaagtgag 2700 gcaactttgt aaactcctta ggggggccaa agcactaaca gacatagtac cactaactga 2760 agaagcagaa ttagaattag cagagaacag ggaaattcta aaagagccag tacatggagt 2820 atattatgac ccatcaaaag acttaatagc tgaaatacag aaacaggggc atgaccaatg 2880 gacatatcaa atttaccaag aaccattcaa aaatctgaaa acagggaagt atgcaaaaat 2940 gaggactgct cacactaatg atgtaaaaca gttaacagag gcagtgcaaa aaatagccat 3000 agaaagcata gtaatatggg aaagacccct aaatttagac tacccatcca aaaagaaacg 3060 tgggagacat ggtggacaga ctattggcag gccacctgga ttcctgattg ggagtttgtt 3120 aatacccctc ccctagtaaa attatggtac cagctagaaa aagaacccat agtaggagca 3180 gaaactttct atgtagatgg agcagctaat agggaaacta aagtaggaaa agcagggtat 3240 gttactgaca gaggaaggca gaaaattgtt tctttaactg aaacaacaaa tcagaagact 3300 gaattgcaag caattcagct agctttgcaa gattcaggaa cagaagtaaa catagtaaca 3360 gactcacagt atgcattagg aatcattcaa gcacaaccag ataaaagtga atcagagtta 3420 gtcaaccaaa taatagaaca attaataaac aaagaaagag tctatctgtc atgggtacca 3480 gcacataaag gaattggagg gaatgaacaa gtagatagat tagtaagtag tggaattagg 3540 aaagtactgt ttctagatgg gatagataag gctcaagaag atcatgaaaa gtatcacagc 3600 aattggagag caatggctaa tgagtttaat ctgccaccca tagtagcaaa agaaatagta 3660 gctagctgtg ataaatgcca gctaaaaggg gaagccatgc atggacaagt agaccgtagc 3720 ccagggatat ggcaattaga ttgtacacat ctagaaggaa aaatcatcct ggtagcagtc 3780 catgtagcca gtggctacat agaagcagag gttatcccag cagaaacagg acaagaaaca 3840 gcatactata tactaaaatt agcaggaaga tggccagtca aagtaataca tacagacaat 3900 ggtagtaatt tcaccagtgc tgcagttaag gcagcctgtt ggtgggcagg tatccaacag 3960 gaatttggaa ttccctacaa tccccaaagc cagggagtag tagaatccat gaataaagaa 4020 ttaaagaaaa ttatagggca ggtaagagaa caagctgagc accttaagac agcagtacaa 4080 atggcagtat tcattcacaa ttttaaaaga aaagggggga ttggggggta cagtgcaggg 4140 gaaagaacaa tagacataat agcaacagac atacaaacta aagaattaca aaaccaaatt 4200 acaaaaattc aaaattttcg ggtttattac agagacagca gagaccccat ttggaaagga 4260 ccagccaaac tgctctggaa aggtgaaggg gcagtagtaa tacaagataa tagtgacata 4320 aaggtagtgc caaggaggaa agcaaaaatt attagggatt atggaaaaca gatggcaggt 4380 gctgattgtg tggcaggtag acaggatgag gatcagaaca tggaatagtt tagtaaaaca 4440 ccatatgtat gtttcaagaa gagctagtgg atggttttac agacatcatt atgaaagcag 4500 acatccaaaa gtaagtgcag aagtacacat cccattagga gatgctagat tagtaataaa 4560 aacatattgg ggtttacaaa caggagaaag agattggcat ttgggtcatg gcgtctccat 4620 agaatggaga ttgggaagat atagcacaca agtagaacct ggcctggcag accagctaat 4680 ccatatgcat tattttgatt gttttgcaga ctctgccata agaaaagcca tattaggaca 4740 catagttatt tctaggtgtg attatcaagc aggacataat aaggtaggat ctctacaata 4800 cttggcactg acagcattga taaaaccaaa aaagagaaag ccacctctgc ctagtgttaa 4860 gaaattagta gaggatagat ggaacaatcc ccagaagacc agggaccaca gagggaacca 4920 tacaatgaat ggacactaga gcttctagag gaactcaagc aggaagctgt cagacacttt 4980 cctagacctt agcttcatag cttaggacaa tatatctatg aaacatatgg ggatgcttgg 5040 acaggagtcg aagctttaat aagaacactg caacaattac tgtttattca tttcagaatt 5100 gggtgccagc atagcagaat aggcatttta caacggagaa gagcaagaaa tggagccagt 5160 agatcctaac ctagagccct ggaaccatcc aggaagtcag cctaaaactg cttgtaatac 5220 atgctattgt aaacactgta gctaccattg tctagtttgc tttcagacaa aaggcttagg 5280 catttcctat ggcaggaaga agcggagaca gcgacgcagc gctcctccaa gcagtgagga 5340 tcatcaaaat cttatatcaa agcagtaagt atatgtaatg gtgaatttat tagaaagagt 5400 agattataga ttaggagtag gagcattaat agtagcatta atcttagcaa taattgtgtg 5460 gaccatagca tatctagaat ataggaaatt gttaagacaa agaaaaataa acaggttaat 5520 tgaaagaatt agggaaagag tagaagacag tggcaatgag agtgaggggg atactgagga 5580 attgtcaaca ctggtggata tggggaatct taggcttttg gatgctaatg atttataatg 5640 tagtagggaa cttgtgggtc acagtctatt atggggtacc tgtgtggaaa gaagcaaaaa 5700 ctactttatt ctgtgcatca gatgctaaag cttatgagaa ggaggtgcat aatatctggg 5760 ctacacatgc ctgtgtaccc acagacccca acccacaaga gatggattta gtaaatgtaa 5820 cagaaaattt taacatgtgg aaaaatgaca tggtggatca gatgcatgag gatgtaatca 5880 gtttatggga tcaaagccta aagccatgtg taaagttgac cccactctgt gtcactttaa 5940 actgtagtaa ggttaccaat aatgctactt acaataatac tgatgatata aaaaattgct 6000 cttttaatgc aaccacagaa ataagagaca agaaacgcaa agagtatgca ctgttttata 6060 gactcgatat agtaccacta aatgagaata agaacagctc tagtaactat agtgagtaca 6120 tattaataaa ttgtaatacc tcaaccataa cacaagcctg tccaaaggtc tcttttgacc 6180 caattcctat acattattgt gctccagctg gttttgcgat tctaaagtgt aaagatgaga 6240 cattcaatgg gacaggacca tgcaaggagg tcagtacagt acaatgtaca catggaatta 6300 agccagtggt atcaactcaa ctactgttaa atggtagcac agcagaaaaa gagataataa 6360 ctagatctga aaatataaca gacaatgcaa aaactataat agtacatctt aatgaatcca 6420 taaaaattgt atgtacaaga cccaacaata acacaagaaa aagtataagg atagggccag 6480 gacaagcatt ctatgcaaca aacggcataa taggagacat aagacaagca cattgtaaca 6540 ttagtgaatc taactggact aaaactttac aagaggtagg aaaaaaatta gcaaagcact 6600 tccctaataa aacaataagt ttcaaccaat cctcaggagg ggacctagaa attgtaacac 6660 atagctttaa ttgtggagga gaattctttt attgtaatac atcaagactg tttaacggta 6720 catacaatgg tacagacatg cctacataca atggtacaaa ttccagttca gacatcatca 6780 tgcttccatg cagaataagg caatttataa acatttggca gaaggtagga cgagcaatgt 6840 atgcccctcc cattgaagga aacataacat gtgaatcaaa tatcacagga ctactattag 6900 tacgtgatgg aggcgacaca aatagtagca cagagatatt cagacctgga ggaggagata 6960 tgagggacaa ttggagaagt gaattatata aatataaagt ggtagaaatt aagccattag 7020 gaatagcacc tactgaagca aaaaggagag tggtggagag agaaaaaaga gcagtgggaa 7080 taggagctgt gttccttggg ttcttgggag tagcaggaag cactatgggc gcggcgtcaa 7140 tgacgctgac ggtacaggcc agacaattgt tgtctggtat agtgcaacag caaagcaatt 7200 tgctgaaggc tatagaggcg caacagcata tgttgcaact cacagtctgg ggcattaagc 7260 agctccagac aagagtcttg gctatagaga gatacctaaa ggatcaacag ctcctaggga 7320 tttggggctg ctctggaaaa gtcatctgcc ccactgctgt gccttggaac tccagctgga 7380 gtaataaatc aaaagatgat atttggaata acatgacctg gatgcagtgg gataaagaga 7440 ttagtaatta cacaaacaca atataccggt tgcttgaaga atcgcaaatc cagcaggaac 7500 aaaatggaaa agatttatta gcattggaca gttggcaaaa tctgtggaat tggtttagca 7560 taacaaaatg gctgtggtat ataaaaatat tcataattat agtaggaggc ttgataggtt 7620 tgagaataat ttttgctgtg ctatctatag taaatagagt taggcaggga tactcacctt 7680 tgtcgttgca gacccttacc ccagacccga gggaacccga caggctcaga ggaatcgaag 7740 aagaaggtgg agagcaagac aaagacagat ccattcgatt agtgaacgga ttcttagcac 7800 ttgcctggga cgatctacgg agcctgtgcc tcttcagttg ccaccgattg agagacttca 7860 tattggttgc agcgagagcg gtggaacttc tgggacgcag cagtctcagg ggactacaga 7920 gggggtggga agcccttaaa tatctgggaa gtcttgtgca gtattggggt ctggaactaa 7980 aaaagagtgc tattagtctg cttgatacca tagcaataac aatagctgag ggaacagata 8040 ggattataga atttacacaa agaatttgca gagctatccg caacatacct agaagaataa 8100 gacagggttt tgaagcagct ttgctataaa atggggagca agatgtcaaa aagcagaata 8160 gttggatggc ctgaggtaag agaaagaatg aggagaactg agccagcagc agagggagta 8220 ggagcagcat ctcaagactt agctaaacat ggagcactta caaccagcaa cacaccaagc 8280 aataatgctg ctggtgcctg gctgcaagcg caagaggagg aagaagaagt aggctttcca 8340 gtcagacctc aggtgccttt aagaccaatg acttataaag gagcattcga tctcgccttc 8400 tttttaaaag aaaagggggg actggatggg ttaatttact ctaagaaaag gcatgaaatc 8460 cttgatttat gggtttataa cacacaaggc tacttccctg attggcaaaa ctacacacca 8520 ggaccagggg tcagatatcc actgaccttt ggatggtgct acaagctagt accagttgac 8580 ccaagtgtag tagaagaggc caacaaagga gaaaacaact gtttgctaca ccctatgagc 8640 caacatggaa tggatgatga agatggagaa gtattaaagt ggcagtttga cagcagccta 8700 gcacgcagac acatagcccg cgagctacat ccggagtatt acaaagactg ctgacacaga 8760 agggactttc cactggggcg ttccagggga gtggtctggg cgggacatgg gagtggtcaa 8820 ccctcagatg ctgcatataa gcagctgctt ttcgcctgta ctgggtctct ctaggtggac 8880 cagatctgag cccgggagct ctctggctac ctagtgaacc cactgcttaa gcctcaataa 8940 agcttgcctt gagtgctct 8959 12 1479 DNA Human immunodeficiency virus type 1 isolate=93BR020; gene=gag 12 atgggtgcga gagcgtcagt attaagcggg ggaaaattag atgcttggga aaaaattcgg 60 ttaaggccgg ggggaaagaa aaaatataga ctaaaacatc tagtatgggc aagcagggag 120 ctagaacgat ttgcacttga tccaggcctt ctagaaacat cagaaggctg tcgaaaaata 180 ataggacagt tacaaccatc ccttcagaca ggatcagaag agctcaaatc attatataat 240 acaatagcag tcctctatta tgtacatcaa aaggtagagg taaaagacac caaggaggct 300 ttagagaagc tagaggaaga acaaaacaaa ggtcggcaaa agacacagca agcgactgct 360 gaaaaagggg tcagtcaaaa ttaccctata gtacagaatc ttcagggaca aatggtacac 420 cagtctttat cacctagaac tttaaatgca tgggtaaagg tgatagaaga gaaggctttt 480 agtccagaag taatacccat gttttcagca ttatcagaag gggccactcc acaagattta 540 aacaccatgt taaatacagt ggggggacat caagcagcca tgcaaatgtt aaaagacacc 600 atcaatgagg aggctgcaga atgggacaga ttacatccaa cacaggcagg acccatcccc 660 ccaggtcaga taagggaacc taggggaagt gatatagctg gaactactag tacccttcag 720 gaacaaatac aatggatgac aggcaaccca cctgtcccag tgggagaaat gtataaaaga 780 tggatcatcc taggattaaa taaaatagta agaatgtata gccctgtcgg cattttggac 840 ataagacaag ggccaaaaga accctttaga gactatgtag acaggttctt taaaacccta 900 agagctgagc aagctacaca ggaagtaaag ggttggatga cagacacctt gttggtccaa 960 aatgcgaacc cagattgtaa gaccatttta aaagcattgg gaccaggggc tacactagag 1020 gaaatgatga cagcatgtca gggagtggga ggacctagcc ataaggcaag agttttggct 1080 gaggcaatga gccaagcaac aaatacagct ataatgatgc agaaaagtaa ctttaagggc 1140 caaagaagaa ttgttaaatg ctttaattgt ggcaaagaag gacacatagc caaaaattgc 1200 agggccccta gaaaaaaggg ctgttggaag tgtggaagag agggacacca aatgaaggac 1260 tgcactgaga gacaggctaa ttttttaggg aaaatttggc cttccaacaa ggggaggccc 1320 ggaaacttca tccagaacag gccagagccg tcagccccgc cagcagagag cttcaggttc 1380 ggggaggaga caaccccatc tccgaagcag gagcagaaag acgagggact gtaccctccc 1440 ttagcttccc tcaaatcact ctttggcaac gacccctag 1479 13 579 DNA Human immunodeficiency virus type 1 isolate=93BR020; gene=vif 13 atggaaaaca gatggcaggt gatgattgtg tggcaggtag acaggatgag gattaacaca 60 tggaaaagtt tagtaaaata ccatatgcat atttcaaaga aagccaaagg atggttttat 120 agacatcact ttgaaagcag gcatccaaaa ataagttcag aagtacacat cccactagag 180 acagctgaat tagtaataac aacatactgg gggctgcttc caggagaaag agaatggcat 240 ctgggtcagg gagtctccat agaatggagg caggggaggt atagaacaca aatagaccct 300 ggcctggcag accaactgat ccatatatat tattttgatt gtttttcaga atctgccata 360 aggaaagcca tattaggaca taaaattagc cctaggtgta actatcaagc aggacataac 420 aaggtaggat ctctacaata cttggcacta acagcattaa tagctccaaa aaagacaaag 480 ccgcctttgc ctagtgtcca gaaactagta gaagacagat ggaacaagcc ccagaagacc 540 aggggccaca gagagagcca tacaatgaat ggacactag 579 14 291 DNA Human immunodeficiency virus type 1 isolate=93BR020; gene=vpr 14 atggaacaag ccccagaaga ccaggggcca cagagagagc catacaatga atggacacta 60 gatcttttag aggagcttaa gaatgaagct gttagacatt ttcctaggcc atggctccat 120 agcttaggac aacatatcta taacacctat ggggatactt gggaaggagt tgaagcaatc 180 ataaggatat tgcaacaact actgtttatc catttcagaa ttgggtgccg tcatagcaga 240 ataggcatta ctcgacagag aagagtaaga aatggaacta gtagatccta a 291 15 2610 DNA Human immunodeficiency virus type 1 isolate=93BR020; gene=tat 15 atggaactag tagatcctaa cttagatccc tggaaccatc caggaagcca gcctacaact 60 ccttgtacca gatgttattg taaatggtgt tgctttcatt gttactggtg ctttacaacg 120 aagggcttag gcatctccta tggcaggaag aagcggagac agcgaccaag aactcctcaa 180 agcagtcaga tacatcaaga ttttgtacca aagcagtaag tattgttaag catatgtaat 240 gtcaaatttg ttagcaatag gcatagcagc attaatagta gcactaataa taacaatagt 300 tgtgtggact atagcatata tagaatataa gaaactggta aggcaaagaa aaataaatag 360 gttatataaa agaataagcg aaagagcaga agacagtggc aatgagagtg agggggatgc 420 agaggaattg gcagcacttg gggaagtggg gccttttatt cctggggaca ttaataatct 480 gtaatgctgc agaaaactta tgggttacag tctattatgg ggtacctgtg tggaaagaag 540 caaccactac tctattctgt gcatcagatg ctaaatcata tgaaaaagag gcacataatg 600 tctgggctac acatgcttgt gtacccacag atcccaatcc acaagaagta gttctggaaa 660 atgtaacaga aaggtttaat atgtgggaaa ataacatggt agaacaaatg catacagata 720 taatcagttt atgggatcaa agcctaaagc catgtgtgaa gttaacccca ctctgtgtta 780 ctttagattg tagaaacatt gccaccaatg gcaccaatga cactattgcc atcaatgaca 840 ctctgaagga agatccagag gcaatacaaa actgttcttt caatacaacc acagaaataa 900 gagataagca gctgaaagta catgcacttt tttataaact tgatatagta caaatcaaca 960 aggatgacaa tagaacatac agactaataa attgtgatgc ctcaaccatt acacaggctt 1020 gtccaaaggt atcttgggat ccaattccca tacattattg tgctccagct ggttatgcga 1080 ttctaaagtg taatgagaaa aatttcacag ggacagggtc atgcaagaat gtcagtacag 1140 tacaatgtac acatggaatt aaaccagtgg tatccactca attgttgtta aatggcagcc 1200 tagcagaagg agagatagta atcagatctc aaaatatctc agataatgca aaaaccataa 1260 tagtgcacct taatgaatct gtacagatta attgtacaag acccaacaac aatacaagaa 1320 aaagaatatc tttaggacca ggacgagtat tttatacaac aggagaaata ataggagaca 1380 tcagaaaggc acattgtaac gttagtggaa cacaatggag gaacacgtta gcaaaggtaa 1440 aggcaaagtt agggtcttat ttccctaatg caacaataaa atttaactca tcctcaggag 1500 gggacctaga aattacaagg cataatttta attgtatggg agaatttttc tactgtaata 1560 cagatgaact gtttaatgac acaaaattca atgacacagg attcaatggc actatcactc 1620 tcccatgtcg aataaaacaa attgtaaaca tgtggcagga agtgggacga gcaatgtatg 1680 ccaatcccat tgcaggaaac attacctgta actcaaatat tacaggtctg ctattgacaa 1740 gagatggtgg tctgaatagt actaatgaga ccttcagacc tgggggagga aatatgaaag 1800 acaattggag aagtgaatta tataaatata aagtagtaga aattgaacca ctaggagtag 1860 cacccaccaa ggcaaaaaga caagtggtga agagagaaag aagagcagtg ggactaggag 1920 ctctgttcct tgggttcttg ggagcagctg gaagcactat gggcgcggcg tcaataacgc 1980 tgacggtaca ggccagacaa ttattgtctg gaatagtgca acagcagagc aatctgctga 2040 gggctattga agcgcaacag catctgttgc agctcacagt ctggggcatt aaacagctcc 2100 aggcaagagt cctggctgtg gaaagatacc taaaggatca acagctccta gggctttggg 2160 gctgctctgg aaaactcatc tgcaccacta atgtgccctg gaactctagt tggagtaata 2220 aatctcttga ggagatttgg gggaacatga cctggatgga gtgggaaaaa gaggttagca 2280 attactcaaa agaaatatac aggttaattg aagactcgca gaaccagcag gaaaagaatg 2340 aacaagaatt attagcattg gacaaatggg caagtctgtg gaattggttt gacataacac 2400 agtggctgtg gtatataaaa atattcataa tgatagtagg aggcttgata ggcttaagaa 2460 tagtttttac tgtgctttct atagtaaata gagttaggaa gggatactca cctttgtcat 2520 ttcagaccca tatcccaagc ccgagggaac ccgacaggcc cgaaggaatc gaagaaggag 2580 gtggagagca aggcaaagac agatccgtga 2610 16 2661 DNA Human immunodeficiency virus type 1 isolate=93BR020; gene=rev 16 atggcaggaa gaagcggaga cagcgaccaa gaactcctca aagcagtcag atacatcaag 60 attttgtacc aaagcagtaa gtattgttaa gcatatgtaa tgtcaaattt gttagcaata 120 ggcatagcag cattaatagt agcactaata ataacaatag ttgtgtggac tatagcatat 180 atagaatata agaaactggt aaggcaaaga aaaataaata ggttatataa aagaataagc 240 gaaagagcag aagacagtgg caatgagagt gagggggatg cagaggaatt ggcagcactt 300 ggggaagtgg ggccttttat tcctggggac attaataatc tgtaatgctg cagaaaactt 360 atgggttaca gtctattatg gggtacctgt gtggaaagaa gcaaccacta ctctattctg 420 tgcatcagat gctaaatcat atgaaaaaga ggcacataat gtctgggcta cacatgcttg 480 tgtacccaca gatcccaatc cacaagaagt agttctggaa aatgtaacag aaaggtttaa 540 tatgtgggaa aataacatgg tagaacaaat gcatacagat ataatcagtt tatgggatca 600 aagcctaaag ccatgtgtga agttaacccc actctgtgtt actttagatt gtagaaacat 660 tgccaccaat ggcaccaatg acactattgc catcaatgac actctgaagg aagatccaga 720 ggcaatacaa aactgttctt tcaatacaac cacagaaata agagataagc agctgaaagt 780 acatgcactt ttttataaac ttgatatagt acaaatcaac aaggatgaca atagaacata 840 cagactaata aattgtgatg cctcaaccat tacacaggct tgtccaaagg tatcttggga 900 tccaattccc atacattatt gtgctccagc tggttatgcg attctaaagt gtaatgagaa 960 aaatttcaca gggacagggt catgcaagaa tgtcagtaca gtacaatgta cacatggaat 1020 taaaccagtg gtatccactc aattgttgtt aaatggcagc ctagcagaag gagagatagt 1080 aatcagatct caaaatatct cagataatgc aaaaaccata atagtgcacc ttaatgaatc 1140 tgtacagatt aattgtacaa gacccaacaa caatacaaga aaaagaatat ctttaggacc 1200 aggacgagta ttttatacaa caggagaaat aataggagac atcagaaagg cacattgtaa 1260 cgttagtgga acacaatgga ggaacacgtt agcaaaggta aaggcaaagt tagggtctta 1320 tttccctaat gcaacaataa aatttaactc atcctcagga ggggacctag aaattacaag 1380 gcataatttt aattgtatgg gagaattttt ctactgtaat acagatgaac tgtttaatga 1440 cacaaaattc aatgacacag gattcaatgg cactatcact ctcccatgtc gaataaaaca 1500 aattgtaaac atgtggcagg aagtgggacg agcaatgtat gccaatccca ttgcaggaaa 1560 cattacctgt aactcaaata ttacaggtct gctattgaca agagatggtg gtctgaatag 1620 tactaatgag accttcagac ctgggggagg aaatatgaaa gacaattgga gaagtgaatt 1680 atataaatat aaagtagtag aaattgaacc actaggagta gcacccacca aggcaaaaag 1740 acaagtggtg aagagagaaa gaagagcagt gggactagga gctctgttcc ttgggttctt 1800 gggagcagct ggaagcacta tgggcgcggc gtcaataacg ctgacggtac aggccagaca 1860 attattgtct ggaatagtgc aacagcagag caatctgctg agggctattg aagcgcaaca 1920 gcatctgttg cagctcacag tctggggcat taaacagctc caggcaagag tcctggctgt 1980 ggaaagatac ctaaaggatc aacagctcct agggctttgg ggctgctctg gaaaactcat 2040 ctgcaccact aatgtgccct ggaactctag ttggagtaat aaatctcttg aggagatttg 2100 ggggaacatg acctggatgg agtgggaaaa agaggttagc aattactcaa aagaaatata 2160 caggttaatt gaagactcgc agaaccagca ggaaaagaat gaacaagaat tattagcatt 2220 ggacaaatgg gcaagtctgt ggaattggtt tgacataaca cagtggctgt ggtatataaa 2280 aatattcata atgatagtag gaggcttgat aggcttaaga atagttttta ctgtgctttc 2340 tatagtaaat agagttagga agggatactc acctttgtca tttcagaccc atatcccaag 2400 cccgagggaa cccgacaggc ccgaaggaat cgaagaagga ggtggagagc aaggcaaaga 2460 cagatccgtg agattagtga ccggattctt agctcttgcc tgggacgacc tgcggaacct 2520 gtgcctcttc agctaccgcc acttgagaga cttcatatta attgcagcga ggattgtgga 2580 cagggggctg aagagggggt gggaagctct caaatatctg gggaatctca cacagtattg 2640 gggtcaggaa ctaaagaata g 2661 17 246 DNA Human immunodeficiency virus type 1 isolate=93BR020; gene=vpu 17 atgtcaaatt tgttagcaat aggcatagca gcattaatag tagcactaat aataacaata 60 gttgtgtgga ctatagcata tatagaatat aagaaactgg taaggcaaag aaaaataaat 120 aggttatata aaagaataag cgaaagagca gaagacagtg gcaatgagag tgagggggat 180 gcagaggaat tggcagcact tggggaagtg gggcctttta ttcctgggga cattaataat 240 ctgtaa 246 18 2541 DNA Human immunodeficiency virus type 1 isolate=93BR020; gene=env 18 atgagagtga gggggatgca gaggaattgg cagcacttgg ggaagtgggg ccttttattc 60 ctggggacat taataatctg taatgctgca gaaaacttat gggttacagt ctattatggg 120 gtacctgtgt ggaaagaagc aaccactact ctattctgtg catcagatgc taaatcatat 180 gaaaaagagg cacataatgt ctgggctaca catgcttgtg tacccacaga tcccaatcca 240 caagaagtag ttctggaaaa tgtaacagaa aggtttaata tgtgggaaaa taacatggta 300 gaacaaatgc atacagatat aatcagttta tgggatcaaa gcctaaagcc atgtgtgaag 360 ttaaccccac tctgtgttac tttagattgt agaaacattg ccaccaatgg caccaatgac 420 actattgcca tcaatgacac tctgaaggaa gatccagagg caatacaaaa ctgttctttc 480 aatacaacca cagaaataag agataagcag ctgaaagtac atgcactttt ttataaactt 540 gatatagtac aaatcaacaa ggatgacaat agaacataca gactaataaa ttgtgatgcc 600 tcaaccatta cacaggcttg tccaaaggta tcttgggatc caattcccat acattattgt 660 gctccagctg gttatgcgat tctaaagtgt aatgagaaaa atttcacagg gacagggtca 720 tgcaagaatg tcagtacagt acaatgtaca catggaatta aaccagtggt atccactcaa 780 ttgttgttaa atggcagcct agcagaagga gagatagtaa tcagatctca aaatatctca 840 gataatgcaa aaaccataat agtgcacctt aatgaatctg tacagattaa ttgtacaaga 900 cccaacaaca atacaagaaa aagaatatct ttaggaccag gacgagtatt ttatacaaca 960 ggagaaataa taggagacat cagaaaggca cattgtaacg ttagtggaac acaatggagg 1020 aacacgttag caaaggtaaa ggcaaagtta gggtcttatt tccctaatgc aacaataaaa 1080 tttaactcat cctcaggagg ggacctagaa attacaaggc ataattttaa ttgtatggga 1140 gaatttttct actgtaatac agatgaactg tttaatgaca caaaattcaa tgacacagga 1200 ttcaatggca ctatcactct cccatgtcga ataaaacaaa ttgtaaacat gtggcaggaa 1260 gtgggacgag caatgtatgc caatcccatt gcaggaaaca ttacctgtaa ctcaaatatt 1320 acaggtctgc tattgacaag agatggtggt ctgaatagta ctaatgagac cttcagacct 1380 gggggaggaa atatgaaaga caattggaga agtgaattat ataaatataa agtagtagaa 1440 attgaaccac taggagtagc acccaccaag gcaaaaagac aagtggtgaa gagagaaaga 1500 agagcagtgg gactaggagc tctgttcctt gggttcttgg gagcagctgg aagcactatg 1560 ggcgcggcgt caataacgct gacggtacag gccagacaat tattgtctgg aatagtgcaa 1620 cagcagagca atctgctgag ggctattgaa gcgcaacagc atctgttgca gctcacagtc 1680 tggggcatta aacagctcca ggcaagagtc ctggctgtgg aaagatacct aaaggatcaa 1740 cagctcctag ggctttgggg ctgctctgga aaactcatct gcaccactaa tgtgccctgg 1800 aactctagtt ggagtaataa atctcttgag gagatttggg ggaacatgac ctggatggag 1860 tgggaaaaag aggttagcaa ttactcaaaa gaaatataca ggttaattga agactcgcag 1920 aaccagcagg aaaagaatga acaagaatta ttagcattgg acaaatgggc aagtctgtgg 1980 aattggtttg acataacaca gtggctgtgg tatataaaaa tattcataat gatagtagga 2040 ggcttgatag gcttaagaat agtttttact gtgctttcta tagtaaatag agttaggaag 2100 ggatactcac ctttgtcatt tcagacccat atcccaagcc cgagggaacc cgacaggccc 2160 gaaggaatcg aagaaggagg tggagagcaa ggcaaagaca gatccgtgag attagtgacc 2220 ggattcttag ctcttgcctg ggacgacctg cggaacctgt gcctcttcag ctaccgccac 2280 ttgagagact tcatattaat tgcagcgagg attgtggaca gggggctgaa gagggggtgg 2340 gaagctctca aatatctggg gaatctcaca cagtattggg gtcaggaact aaagaatagt 2400 gctattagct tgcttaatgc cacagcaata gcagtagctg agtggacaga tagagttata 2460 gaagctttgc aaagagctgg tagagctatt ctcaacatac ctagaagaat aagacagggc 2520 ttggaaaggg ctttgctata a 2541 19 27 DNA Human immunodeficiency virus type 1 isolate=93BR020; gene=nef 19 atgggtggca agtggtcaaa aagtagt 27 20 8 DNA Human immunodeficiency virus type 1 isolate=93BR020; gene=gag-pol fusion 20 aaaaaaaa 8 21 207 DNA Human immunodeficiency virus type 1 isolate=92NG083; gene=gag 21 gtgggtgcga gagcgtcagt attaagcggg ggaaaattag attcttggga aaaaattcgg 60 ttaaggccag ggggaaggaa aaagtataaa ctaaaacata tagtatgggc aagcagggaa 120 ctggggagat ttgcacttaa ccgtgacctt ttagaaacag cagaaggttg tgtgcaaata 180 atgaaacagt tgcaaccagc tctctag 207 22 2739 DNA Human immunodeficiency virus type 1 isolate=92NG083; gene=pol; note=NH2-terminus uncertain 22 ataaatttac caggaaaatg gaaaccaaaa atgatagggg gaattggagg ttttatcaaa 60 gtaagacagt atgatcaaat acttatagaa attggtggaa aaaaggctat agggacagta 120 ttagtaggac ctacacctat taacataatt gggagaaata tgttgactca gattggttgt 180 actttaaact ttccaataag tcctattgaa actgtaccag taaaattaaa gccaggaatg 240 gatggcccaa gggttaaaca atggccattg acagaagaga aaataaaagc attaacagaa 300 atttgtaaag acatggaaaa ggaaggaaaa atttcaaaaa ttgggcctga aaatccatat 360 aacactccaa tattcgccat aaagaaaaaa gacagtacta aatggagaaa attggtagat 420 ttcagagaac ttaataaaag aactcaagac ttctgggagg tccaattagg aatacctcac 480 cccgcggggt taaaaaagaa aagatcagta acggtactag atgtgggaga tgcatacttt 540 tcagttccct tagataaaga ctttagaaag tatactgcat ttactatacc tagtataaat 600 aatgagacac cagggattag atatcaatac aatgtgcttc cacagggatg gaaaggatca 660 ccagcaatat ttcagagtag catgacaaaa attttagagc cttctagaac aaaaaatcca 720 gaaatggtga tctaccaata catggatgat ttatatgtag gatctgactt agaaataggg 780 cagcatagag caaaaataga ggagttaaga gaacatctac tgaaatgggg attgaccaca 840 ccagataaaa aacatcagaa agaacctcca ttcctttgga tgggatatga gctccatcct 900 gacaaatgga cggtacaacc tatacagctg ccagaaaagg aagattggac tgtcaatgat 960 atacaaaagt tagtgggaaa actaaattgg gcaagtcaga tttatccagg gattaaagta 1020 aagcacctat gtagactcct taggggggcc aaagcactaa cagacatagt acccctaacg 1080 gcagaagcag aaatggagct ggcagagaac agggaaattc taaaagaacc tgtacatgga 1140 gtctatcatg acccatcaaa agaattaata gcagaagtac agaagcaagg gccagaccaa 1200 tggacatatc aaatttatca agagccatac aaaaatctaa aaacaggaaa atatgcaaaa 1260 agggggtctg cccacactaa tgatgtaaaa caattaacag aagtagtgca aaaaatagcc 1320 acagagggca tagtaatctg gggaaagatt cctaaattta aactacctat acgaaaagaa 1380 acatgggaag tatggtggac agagtactgg caggccgcct ggattcctga gtgggagttt 1440 gtcaataccc ctcctctagt aaaactatgg tatcaattag aaacagaacc cataccagga 1500 gcagaaactt actatgtaga tggggcagct aatagggaga caaaattagg aaaggcagga 1560 catgttactg acaaaggaaa acaaaaaatt attaccctaa ctgaaacaac aaaccaaaag 1620 gctgaattac atgcaattca actagctttg caggactcaa gaccagaagt aaacatagta 1680 acagactcac agtatgcatt aggaatcatt caagcacaac cagataggag tggatcagaa 1740 ttagtcaatc aaataataga acagctaata aaaaaggaaa aggtctacct gtcatgggta 1800 ccagcacaca aagggattgg aggaaatgaa caagtagata agctagtcag tagtggaatc 1860 aggaaagtat tatttttgga tggcatagat aaagcccaag aagaacatga aagatatcac 1920 agcaattgga gagcaatggc tagtgatttt aatctgccac ctgtagtagc aaaagaaata 1980 gtggccagct gtgataaatg tcaactaaaa ggggaagcca tgcatggaca agtagactgt 2040 agtccaggaa tatggcaatt agattgtaca catttagaag gaaaaattat catagtagca 2100 gttcatgtag ccagtggcta tatagaagca gaagttatcc cagcagaaac agggcaggaa 2160 acagcatact ttatattaaa attagcagga aggtggccag taaaagtgat acatacagac 2220 aatggtccca atttcatcag tgctgcagta aaggcagcat gttggtgggc aaatatcaca 2280 caggaatttg gaattcccta caatccccaa agccaaggag tagtggaatc tatgaataag 2340 gaattaaaga aaatcatcgg acaggttgga gatcaagctg aacatcttaa gacagcagta 2400 cagatggcag tattcattca caattttaaa agaaaagggg ggattggggg gtacagtgca 2460 ggggaaagaa taatagacat aatagcatca gatatacaaa ctaaagaact acaaaaacaa 2520 attataaaaa ttcaaaattt tcgggtttat tacagggaca gcagagaccc aatttggaaa 2580 ggaccagcaa agctactctg gaaaggtgaa ggggcagtag taatacagga caataacgaa 2640 ataaaggtag taccaagaag aaaagcaaag atccttaagg attatggaaa acagatggca 2700 ggtggtgatt gtgtggcagg tagacaggat gaggattag 2739 23 579 DNA Human immunodeficiency virus type 1 isolate=92NG083; gene=vif 23 atggaaaaca gatggcaggt ggtgattgtg tggcaggtag acaggatgag gattagaaca 60 tggaacagtt tagtaaaaca tcatatgtat gtctcaaaga aagctaaagg ctggttttat 120 agacatcact atgaaagcag gcatccaaga gtaagttcag aagtacacat cccactaaga 180 gatgctacac tagtagtaag aacatattgg ggtctgcatg caggagaaaa agactggcaa 240 ttgggccatg gggtttccat agaatggagg cagaaaagat atagtacaca aatagaccct 300 aacacagcag accatctgat tcatctgtat tattttgact gtttttcaga atctgccata 360 agaaaagcca tattaggaga gatagttagc cctaggtgtg aatacccagc aggacataat 420 aaggtaggat ctctacaata tctggcatcg aaagcattag taacaccaac aaggaaaagg 480 ccacctttgc caagtgttgg gaaattagca gaagatagat ggaacaagcc ccagaagacc 540 agggaccaca gagagaaccc tacaatgaat ggacattag 579 24 291 DNA Human immunodeficiency virus type 1 isolate=92NG083; gene=vpr 24 atggaacaag ccccagaaga ccagggacca cagagagaac cctacaatga atggacatta 60 gaactgttag aagagcttaa aaatgaagct gttagacatt ttcctaggcc ctggctccat 120 ggcttaggac agtatatcta taacacttat ggggatactt gggaaggagt tgaagccata 180 ataagaatac tacaacaact actgtttatc catttcagaa tcgggtgcca acatagcaga 240 ataggcatta ctccacagag aagagtaagg gatggacccg gtagacccta a 291 25 2597 DNA Human immunodeficiency virus type 1 isolate=92NG083; gene=tat 25 atggacccgg tagaccctaa gctagagccc tggaatcatc cggggagtca gcctacaact 60 ccctgtaaca aatgttattg taaagtgtgc tgctggcatt gtcaagtttg ctttttaaac 120 aaaggcttag gcatctccta tggcaggaag aagcggagac cccgacgagg aactcctcag 180 ggcagtaagg atcatcaaaa ccctgtacca aagcagtaag tagtaacaat taatatatgt 240 aatgcaggcc ttagaaatat ctgactaata gtagcattca tagcagccac aattgtgtgg 300 agtatagtat ttatagaata tagaaaaata agaaaacaga aaaaaataga aaagttactt 360 gatagaataa gagaaagagc agaagacagt ggaaatgaga gtgaagggga tacagaggaa 420 ttggcaacac ttatggaaat gggggacttt gatccttggg ttggtaataa tttgtagtgc 480 ctcagataac ttgtgggtca cagtctatta tggggtacct gtgtgggaag atgcagatac 540 ccccctattc tgtgcctctg atgctaaatc atatagttct gaaaaacata atgtctgggc 600 tacacatgcc tgtgtaccca cagaccctaa cccacaagaa atagctatag aaaatgtaac 660 agaaaatttt aacatgtgga agaataacat ggtagaacag atgcaggagg atataatcag 720 tttatgggag gaaagcctaa agccatgtgt aaagctaact cctctctgta tcactttaaa 780 ctgtactaat gtaaacagtg ctaatcatac tgaggccaat aacactgtag aaaacaaaga 840 agaaataaaa aactgctctt tcaagataac cacagaaagg ggaggcaaga agaaggaaga 900 atacgcgctt ttctataaac ttgatgtggt accaattagt aatgggaata agactagtta 960 taggctaata cattgtaatg tctcaaccat taaacaggct tgtccaaagg taaattttga 1020 cccaattccc atacattatt gtgctccagc tggttttgcg attttaaagt gtagggataa 1080 ggagtacaat ggaacaggac catgtaaaaa tgtcagtaca gtacaatgta cacatggaat 1140 taagccagtg gtatcaactc aactactgct gaatggcagt ttagcagaag aagatataag 1200 aattagatct gaaaatttca cagacaatac caaagtcata atagtgcagc ttaataatag 1260 tatagaaatt aattgtatca gacccaataa caatacaaga aaaagtatac caatcggacc 1320 aggacaagcg ttctatgcaa caggtgatat aataggagac ataagacaag cacattgtaa 1380 tgttagtaga ataaaatgga gggagatgtt aaagaatgtc acagcacagc taaggaaaat 1440 ctataataat aagaacataa cctttaactc atctgcagga ggggacctag aaattacaac 1500 acatagtttc aattgtagag gagagttttt ctattgcaat acatcaggac tgtttaataa 1560 taatattagt aatattaata atgagactat cacactccca tgtaaaataa aacaaattgt 1620 gaggatgtgg cagaaagtgg gacaagcaat gtatgccctt cccatcgcag gaaaccttgt 1680 atgtaaatca aacattacag gattaatatt aacaagagat ggtgggaata acaatgacag 1740 tacagaggag accttcagac ctggaggagg agatatgagg gacaattgga gaagtgaatt 1800 atataagtat aaaacagtaa aaatcaaatc actaggagta gcacccacca gggcaaggag 1860 aagagtggtg gagagagaaa aaagagcagt tggactggga gctgtcttcc ttgggttctt 1920 aggagcagca gggagcacta tgggcgcggc gtcaataacg ctgacggcac aggtcagaca 1980 attattgtct ggcatagtgc aacagcaaag caatttgctg agggctatag aggcgcagca 2040 gcatctgttg caactcacag tctggggcat taaacagctc cagtcaagag tcctggctat 2100 agaaagatac ctaaaggatc aacagctcct agggatttgg ggctgctctg gaaaactcat 2160 ctgcaccact aatgtgccct ggaacactag ttggagtaat aaatcttata atgagatttg 2220 ggataacatg acttggctag aatgggaaag ggaaattcac aattacacac aacacatata 2280 cagcctgatt gaagaatcgc agaaccagca ggaaaagaat gaacaagact tattggcatt 2340 ggacaagtgg gcaagtttgt ggaattggtt tgacatatca aattggctat ggtatataag 2400 aatattcata atgatagtag gaggtttaat aggtttaaga atagtttttg ctgtgctttc 2460 tatagtaaat agagttaggc agggatactc acctttgtcg ttccagaccc ttacccatca 2520 ccagcgggaa cccgacaggc tcggaaaaac cgaagaagga ggtggcgagc aagacagaga 2580 cagatccact cgattag 2597 26 2663 DNA Human immunodeficiency virus type 1 isolate=92NG083; gene=rev 26 atggcaggaa gaagcggaga ccccgacgag gaactcctca gggcagtaag gatcatcaaa 60 accctgtacc aaagcagtaa gtagtaacaa ttaatatatg taatgcaggc cttagaaata 120 tctgactaat agtagcattc atagcagcca caattgtgtg gagtatagta tttatagaat 180 atagaaaaat aagaaaacag aaaaaaatag aaaagttact tgatagaata agagaaagag 240 cagaagacag tggaaatgag agtgaagggg atacagagga attggcaaca cttatggaaa 300 tgggggactt tgatccttgg gttggtaata atttgtagtg cctcagataa cttgtgggtc 360 acagtctatt atggggtacc tgtgtgggaa gatgcagata cccccctatt ctgtgcctct 420 gatgctaaat catatagttc tgaaaaacat aatgtctggg ctacacatgc ctgtgtaccc 480 acagacccta acccacaaga aatagctata gaaaatgtaa cagaaaattt taacatgtgg 540 aagaataaca tggtagaaca gatgcaggag gatataatca gtttatggga ggaaagccta 600 aagccatgtg taaagctaac tcctctctgt atcactttaa actgtactaa tgtaaacagt 660 gctaatcata ctgaggccaa taacactgta gaaaacaaag aagaaataaa aaactgctct 720 ttcaagataa ccacagaaag gggaggcaag aagaaggaag aatacgcgct tttctataaa 780 cttgatgtgg taccaattag taatgggaat aagactagtt ataggctaat acattgtaat 840 gtctcaacca ttaaacaggc ttgtccaaag gtaaattttg acccaattcc catacattat 900 tgtgctccag ctggttttgc gattttaaag tgtagggata aggagtacaa tggaacagga 960 ccatgtaaaa atgtcagtac agtacaatgt acacatggaa ttaagccagt ggtatcaact 1020 caactactgc tgaatggcag tttagcagaa gaagatataa gaattagatc tgaaaatttc 1080 acagacaata ccaaagtcat aatagtgcag cttaataata gtatagaaat taattgtatc 1140 agacccaata acaatacaag aaaaagtata ccaatcggac caggacaagc gttctatgca 1200 acaggtgata taataggaga cataagacaa gcacattgta atgttagtag aataaaatgg 1260 agggagatgt taaagaatgt cacagcacag ctaaggaaaa tctataataa taagaacata 1320 acctttaact catctgcagg aggggaccta gaaattacaa cacatagttt caattgtaga 1380 ggagagtttt tctattgcaa tacatcagga ctgtttaata ataatattag taatattaat 1440 aatgagacta tcacactccc atgtaaaata aaacaaattg tgaggatgtg gcagaaagtg 1500 ggacaagcaa tgtatgccct tcccatcgca ggaaaccttg tatgtaaatc aaacattaca 1560 ggattaatat taacaagaga tggtgggaat aacaatgaca gtacagagga gaccttcaga 1620 cctggaggag gagatatgag ggacaattgg agaagtgaat tatataagta taaaacagta 1680 aaaatcaaat cactaggagt agcacccacc agggcaagga gaagagtggt ggagagagaa 1740 aaaagagcag ttggactggg agctgtcttc cttgggttct taggagcagc agggagcact 1800 atgggcgcgg cgtcaataac gctgacggca caggtcagac aattattgtc tggcatagtg 1860 caacagcaaa gcaatttgct gagggctata gaggcgcagc agcatctgtt gcaactcaca 1920 gtctggggca ttaaacagct ccagtcaaga gtcctggcta tagaaagata cctaaaggat 1980 caacagctcc tagggatttg gggctgctct ggaaaactca tctgcaccac taatgtgccc 2040 tggaacacta gttggagtaa taaatcttat aatgagattt gggataacat gacttggcta 2100 gaatgggaaa gggaaattca caattacaca caacacatat acagcctgat tgaagaatcg 2160 cagaaccagc aggaaaagaa tgaacaagac ttattggcat tggacaagtg ggcaagtttg 2220 tggaattggt ttgacatatc aaattggcta tggtatataa gaatattcat aatgatagta 2280 ggaggtttaa taggtttaag aatagttttt gctgtgcttt ctatagtaaa tagagttagg 2340 cagggatact cacctttgtc gttccagacc cttacccatc accagcggga acccgacagg 2400 ctcggaaaaa ccgaagaagg aggtggcgag caagacagag acagatccac tcgattagtg 2460 agcggattct tagcgcttgc ctgggacgac ctgcggagcc tgtgcctttt cagctaccac 2520 cgcttgaggg acttagtctt gattgcagca aggacggtgg aacttctggg acgcagcagc 2580 ctcaagggac tgagactggg gtgggaaggc ctcaagtact tgtggaacct cctgttgtat 2640 tggggtcggg aactaaagaa tag 2663 27 26 DNA Human immunodeficiency virus type 1 isolate=92NG083; gene=vpu (defective); note=10 bp deletion early in vpu frameshifts, results in premature termination 27 tgcaggcctt agaaatatct gactaa 26 28 2550 DNA Human immunodeficiency virus type 1 isolate=92NG083; gene=env 28 atgagagtga aggggataca gaggaattgg caacacttat ggaaatgggg gactttgatc 60 cttgggttgg taataatttg tagtgcctca gataacttgt gggtcacagt ctattatggg 120 gtacctgtgt gggaagatgc agataccccc ctattctgtg cctctgatgc taaatcatat 180 agttctgaaa aacataatgt ctgggctaca catgcctgtg tacccacaga ccctaaccca 240 caagaaatag ctatagaaaa tgtaacagaa aattttaaca tgtggaagaa taacatggta 300 gaacagatgc aggaggatat aatcagttta tgggaggaaa gcctaaagcc atgtgtaaag 360 ctaactcctc tctgtatcac tttaaactgt actaatgtaa acagtgctaa tcatactgag 420 gccaataaca ctgtagaaaa caaagaagaa ataaaaaact gctctttcaa gataaccaca 480 gaaaggggag gcaagaagaa ggaagaatac gcgcttttct ataaacttga tgtggtacca 540 attagtaatg ggaataagac tagttatagg ctaatacatt gtaatgtctc aaccattaaa 600 caggcttgtc caaaggtaaa ttttgaccca attcccatac attattgtgc tccagctggt 660 tttgcgattt taaagtgtag ggataaggag tacaatggaa caggaccatg taaaaatgtc 720 agtacagtac aatgtacaca tggaattaag ccagtggtat caactcaact actgctgaat 780 ggcagtttag cagaagaaga tataagaatt agatctgaaa atttcacaga caataccaaa 840 gtcataatag tgcagcttaa taatagtata gaaattaatt gtatcagacc caataacaat 900 acaagaaaaa gtataccaat cggaccagga caagcgttct atgcaacagg tgatataata 960 ggagacataa gacaagcaca ttgtaatgtt agtagaataa aatggaggga gatgttaaag 1020 aatgtcacag cacagctaag gaaaatctat aataataaga acataacctt taactcatct 1080 gcaggagggg acctagaaat tacaacacat agtttcaatt gtagaggaga gtttttctat 1140 tgcaatacat caggactgtt taataataat attagtaata ttaataatga gactatcaca 1200 ctcccatgta aaataaaaca aattgtgagg atgtggcaga aagtgggaca agcaatgtat 1260 gcccttccca tcgcaggaaa ccttgtatgt aaatcaaaca ttacaggatt aatattaaca 1320 agagatggtg ggaataacaa tgacagtaca gaggagacct tcagacctgg aggaggagat 1380 atgagggaca attggagaag tgaattatat aagtataaaa cagtaaaaat caaatcacta 1440 ggagtagcac ccaccagggc aaggagaaga gtggtggaga gagaaaaaag agcagttgga 1500 ctgggagctg tcttccttgg gttcttagga gcagcaggga gcactatggg cgcggcgtca 1560 ataacgctga cggcacaggt cagacaatta ttgtctggca tagtgcaaca gcaaagcaat 1620 ttgctgaggg ctatagaggc gcagcagcat ctgttgcaac tcacagtctg gggcattaaa 1680 cagctccagt caagagtcct ggctatagaa agatacctaa aggatcaaca gctcctaggg 1740 atttggggct gctctggaaa actcatctgc accactaatg tgccctggaa cactagttgg 1800 agtaataaat cttataatga gatttgggat aacatgactt ggctagaatg ggaaagggaa 1860 attcacaatt acacacaaca catatacagc ctgattgaag aatcgcagaa ccagcaggaa 1920 aagaatgaac aagacttatt ggcattggac aagtgggcaa gtttgtggaa ttggtttgac 1980 atatcaaatt ggctatggta tataagaata ttcataatga tagtaggagg tttaataggt 2040 ttaagaatag tttttgctgt gctttctata gtaaatagag ttaggcaggg atactcacct 2100 ttgtcgttcc agacccttac ccatcaccag cgggaacccg acaggctcgg aaaaaccgaa 2160 gaaggaggtg gcgagcaaga cagagacaga tccactcgat tagtgagcgg attcttagcg 2220 cttgcctggg acgacctgcg gagcctgtgc cttttcagct accaccgctt gagggactta 2280 gtcttgattg cagcaaggac ggtggaactt ctgggacgca gcagcctcaa gggactgaga 2340 ctggggtggg aaggcctcaa gtacttgtgg aacctcctgt tgtattgggg tcgggaacta 2400 aagaatagtg ctattaattt gcttgataca atagcaatag caacagctaa cgggacagat 2460 agggttatag aagtagcaca aagagcttat agagctattc tcaacgtacc tacaaggata 2520 agacaaggct tagaaagagc tttgctataa 2550 29 1503 DNA Human immunodeficiency virus type 1 isolate=90CR056; gene=gag; CDS join(137..1434,1434..4443) 29 atgggtgcga gagcgtcagt attaagcggc ggaaaattag atgcttggga gaaaattcgg 60 ctaaggccag ggggaaagaa aaaatatagg ctaaaacatc tagtatgggc aagcagggag 120 ctggaaagat ttgcacttaa ccccggcctt ttagaaacac cagaaggctg tctacagata 180 atagaacaga tacagccagc tattaagaca ggaacagaag aacttaaatc attatttaat 240 ctagtagcag tcctctattg cgtacatcga aaaatagatg tgaaagacac caaggaggct 300 ttagataaga tagaggaaat acaaaacaaa agtcagcaaa aaacacagca agcagcagct 360 gataaggaaa aagacaacaa ggtcagtcaa aattatccta tagtacagaa tgctcaaggg 420 cagatggtac accaggccat atcacctagg accttaaatg catgggtaaa agtagtagaa 480 gaaaaggctt ttagcccaga agtaataccc atgttttcag cattatcaga aggagccacc 540 ccacaagact taaatgctat gctaaataca gtggggggac atcaagcagc catgcagatg 600 ttaaaagata caatcaatga ggaagctgca gaatgggaca gggtacatcc agtgcatgca 660 gggcctattc caccaggcca aatgagagaa ccaaggggaa gcgatatagc aggaactact 720 agtaccctgc aggaacaaat agcatggatg acaggcaatc cagctatccc agtgggagac 780 atctataaaa gatggataat cctgggatta aataagatag taagaatgta tagtcctgtc 840 agcattctgg acataaaaca agggccaaaa gaacccttta gagactatgt agacaggttt 900 tttaaaactt taagagctga gcaagccaca caggatgtga agaattggat gacagaaacc 960 ttgttggtcc aaaatgcaaa tccagattgc aagactatat taagagcatt aggacaaggg 1020 gcttcaatag aagaaatgat gacagcatgt cagggagtgg gaggacctag tcataaagca 1080 agagttttgg ctgaggcaat gagccaagta acaaatacaa atacagccat aatgatgcag 1140 aaaggcaact ttaagggcca aagaaaattt gttaaatgct tcaactgtgg caaagaggga 1200 cacatagcca gaaattgcag ggcccctagg aaaaagggct gttggaaatg tggaagagaa 1260 ggacatcaga tgaaagactg cacagagaga caggctaatt ttttagggaa aatttggcct 1320 tccagcaaag ggaggccagg aaattttctc cagagcaggc cagaaccaac agccccacca 1380 gcagagagct tcgggttcgg agaggagatg accccctctc cgaagcagga gcagctgaag 1440 gacaaggaac ctcccttagc ttccctcaga tcactctttg gcagcgaccc cttgttacag 1500 taa 1503 30 579 DNA Human immunodeficiency virus type 1 isolate=90CR056; gene=vif 30 atggaaaaca gatggcaggt gatgattgtg tggcaagtag acaggatgag gattaacaca 60 tggaaaagct tagtaaagta ccatatgcat atttcaagga aagctagagg atggttttat 120 agacatcatt ttgaaagcac tcatccaagg ataagttcag aagtacacat cccattagga 180 gaagctaggt tagtcataac cacatactgg ggtctgaata caggagaaag agaatggcat 240 ttaggccagg gagtctccat agaatggaga ctgaaaaggt atagcacaca agtagagcct 300 ggcctggcag accaactaat tcatatgcat tattttgatt gtttttcaga atctgccata 360 aggaaagcca tattaggacg tgtagttaga cctaggtgta actatccagc aggacataaa 420 caggtaggaa ctctacaata cttggcatta acagcattag tggcaccaaa aaagataaag 480 ccacctttgc ctagtgttag aaagctagta gaggatagat ggaacaagcc ccagaagacc 540 aggggccaca gagggagcca cacaatgaat ggacactag 579 31 291 DNA Human immunodeficiency virus type 1 isolate=90CR056; gene=vpr 31 atggaacaag ccccagaaga ccaggggcca cagagggagc cacacaatga atggacacta 60 gagcttttag aggagattaa gaatgaggct gttaggcatt ttcctagagt atggctccat 120 caattaggac agcatatcta taacacctat ggagatactt gggtaggagt tgaagcttta 180 ataagaacgc tgcaacaact actgtttatt catttcagaa ttgggtgcca acatagcaga 240 ataggaatta ctcgacagag aagagtaaga aatggaccca gtagatccta a 291 32 624 DNA Human immunodeficiency virus type 1 isolate=92NG083; gene=nef 32 atggggggca agtggtcaaa aagtagcata gttggatggc ctcagataag ggaaagaata 60 agacaaactc ctgtagcagc agaaggagta ggagcagtat ctcaagattt agctaggcat 120 ggagcaatca caagcagcaa tacagcaacc aacaatcctg attgtgcctg gctggaagca 180 caagaggagg actcagatgt aggctttccg gtcagaccac aggtaccttt gagaccaatg 240 acttataagg ctgcttttga tctcagcttc tttttaaaag aaaagggggg actggatggg 300 ctaatttact ccaagagaag acaagacatc cttgatctat gggtctataa tacacaagga 360 ttcttcccag attggcagaa ctacacacca gggccaggga ctagactccc actgaccttt 420 gggtggtgct tcaaactagt accaatggac ccagcagaga tagaggaagc caataaggga 480 gagaacatca gtctattaca ccccatctgc cagcatggaa tggaggatga agacagagaa 540 gtgctggtat ggagatttaa cagtagccta gcacggagac acctagcccg agagctgcat 600 ccggagtact acaaagactg ctga 624 33 2606 DNA Human immunodeficiency virus type 1 isolate=90CR056; gene=tat; CDS join (5177..5391, 7698..7782) 33 atggacccag tagatcctaa actagagccc tggaaccatc caggaagtca gcctcaaact 60 gcttgtaaca attgttattg taaaaagtgc tgctatcatt gccaaatgtg ctttttaaag 120 aaaggcttag gaatttccta tggcaggaag aagcggagcc agcgacacag aactcctgca 180 agtttgcaag atcatcaaaa ttctatatca aagcagtaag tattatcata aatgtatata 240 ttaggattag gaataggagc gctagtagta acatttatca tagccgtaat tgtgtggacc 300 atagtatata tagaatataa aaaattggta aggcaaaaga aaatagacag gctaattgaa 360 agaataggag aaagagcaga agacagtggc aacgagagtg atggagacac agaggaatta 420 tccaagctta tggagatggg gcaccttaat cttgggtatg ttgctgatct gtagtgctgc 480 acaaaacttg tgggttacag tatattatgg ggtacctgtg tggaaagagg caaaaaccac 540 tctattctgt gcatcagatg ctaaggcata tgagacagaa aagcataatg tctgggctac 600 acatgcatgt gtacccacag accccaaccc acaagagatg gtcatggaga atgtaacaga 660 gagctttaat atgtgggaaa ataacatggt ggagcagatg catacagaca taatcagttt 720 atgggatcaa agcttgaaac catgtgtaaa attaacccca ctctgtgtta ctctaaactg 780 tactaatgtc agaaacaata cctctaacag cactagcagt atggaggcag gaggggaact 840 aacaaattgc tctttcaatg taactacagt actaagagat aagcagcaga aagtacatgc 900 actcttttat agacttgatg tagtaccaat tgataacaat agtactcagt ataggctaat 960 aaattgtaat acctcagtca ttacacaggc ttgcccaaag gtgtcctttg aacctattcc 1020 catacattat tgtgctccag ctggctttgc gattctaaag tgtaacaata aaacattcaa 1080 tggaacagga ttatgtacaa atgtcagtac agtacaatgt acacatggaa ttagaccagt 1140 ggtatcaact caactgctat taaatggaag cctagcagaa gaacagatca taattagaac 1200 taaaaatatc tcagacaata ccaaaaacat aatagtacag cttaagacac cagtaaacat 1260 tacatgtacc aggcctaaca ataatacgag aacaagtata catttagggc caggacgagc 1320 attctatgca acaggtgaca tcataggaga tataagacaa gcacattgta atattagtag 1380 aacagactgg aataagactt tacaccaggt agttacacaa ttaggaatac acttgaacaa 1440 tagaacaata agctttaagc caaactcagg aggggacatg gaagttagaa cacatagttt 1500 taattgtaga ggagaatttt tctattgcaa tacatcaggg ctgtttaata gtagttggga 1560 aatgcatact aattacacat caaatgacac aaagggaaac gaaaacatta cactgccatg 1620 cagaataaaa caaattgtaa acatgtggca gagagtagga cgagcaatgt atgcccctcc 1680 catccaagga aacattatgt gtgtatcaaa tattacagga ctaatattga caattgacga 1740 gggtaacgcg tctgcagaaa attatacctt cagacctgga ggaggagata tgagggacaa 1800 ttggagaagt gaattgtata aatataaagt agtaaaaatt gaaccactgg gaatagcacc 1860 caccaagaca aggagaagag tggtggagag agaaaaaaga gcagtgggaa tgggagcttc 1920 tttccttggg ttcttgggag cagcaggaag cactatgggc gcggcgtcaa taacgctgac 1980 ggtacaggcc aggcaattat tgtctggtat agtgcagcag caaagcaatt tgctgagagc 2040 tatacaggcg cgacagcata tgttgcagct cacggtctgg ggcattaaac agctccaggc 2100 aagagtcctc gctgtggaaa gatacctaag ggatcaacag ctcctgggga tttggggctg 2160 ctctggaaaa ctcatctgca ccactaatgt gccttggaac tctagttgga gtaataaatc 2220 acagagtgaa atctgggaca acatgacttg gatggaatgg gataaacaaa ttagcaatta 2280 cacagaggaa atatacaggt tgcttgaagt ctcgcaaacc cagcaggaaa agaatgaaca 2340 ggacttatta gcattggaca aatgggcaag tctgtggact tggtttgaca tatcacattg 2400 gctgtggtat ataaaaatat tcataatgat agtaggaggt ttaataggtt taagaataat 2460 ttttgctgtg ctttctatag taaatagagt taggcaggga tactcacctt tgtcttttca 2520 gacccttgtc ccgaacccac ggggacccga caggcccgaa ggaacagaag aaggaggtgg 2580 cgagcaagac agagacagat ccgtga 2606 34 2657 DNA Human immunodeficiency virus type 1 isolate=90CR056; gene=rev; CDS join(5316..5391, 7698..7972) 34 atggcaggaa gaagcggagc cagcgacaca gaactcctgc aagtttgcaa gatcatcaaa 60 attctatatc aaagcagtaa gtattatcat aaatgtatat attaggatta ggaataggag 120 cgctagtagt aacatttatc atagccgtaa ttgtgtggac catagtatat atagaatata 180 aaaaattggt aaggcaaaag aaaatagaca ggctaattga aagaatagga gaaagagcag 240 aagacagtgg caacgagagt gatggagaca cagaggaatt atccaagctt atggagatgg 300 ggcaccttaa tcttgggtat gttgctgatc tgtagtgctg cacaaaactt gtgggttaca 360 gtatattatg gggtacctgt gtggaaagag gcaaaaacca ctctattctg tgcatcagat 420 gctaaggcat atgagacaga aaagcataat gtctgggcta cacatgcatg tgtacccaca 480 gaccccaacc cacaagagat ggtcatggag aatgtaacag agagctttaa tatgtgggaa 540 aataacatgg tggagcagat gcatacagac ataatcagtt tatgggatca aagcttgaaa 600 ccatgtgtaa aattaacccc actctgtgtt actctaaact gtactaatgt cagaaacaat 660 acctctaaca gcactagcag tatggaggca ggaggggaac taacaaattg ctctttcaat 720 gtaactacag tactaagaga taagcagcag aaagtacatg cactctttta tagacttgat 780 gtagtaccaa ttgataacaa tagtactcag tataggctaa taaattgtaa tacctcagtc 840 attacacagg cttgcccaaa ggtgtccttt gaacctattc ccatacatta ttgtgctcca 900 gctggctttg cgattctaaa gtgtaacaat aaaacattca atggaacagg attatgtaca 960 aatgtcagta cagtacaatg tacacatgga attagaccag tggtatcaac tcaactgcta 1020 ttaaatggaa gcctagcaga agaacagatc ataattagaa ctaaaaatat ctcagacaat 1080 accaaaaaca taatagtaca gcttaagaca ccagtaaaca ttacatgtac caggcctaac 1140 aataatacga gaacaagtat acatttaggg ccaggacgag cattctatgc aacaggtgac 1200 atcataggag atataagaca agcacattgt aatattagta gaacagactg gaataagact 1260 ttacaccagg tagttacaca attaggaata cacttgaaca atagaacaat aagctttaag 1320 ccaaactcag gaggggacat ggaagttaga acacatagtt ttaattgtag aggagaattt 1380 ttctattgca atacatcagg gctgtttaat agtagttggg aaatgcatac taattacaca 1440 tcaaatgaca caaagggaaa cgaaaacatt acactgccat gcagaataaa acaaattgta 1500 aacatgtggc agagagtagg acgagcaatg tatgcccctc ccatccaagg aaacattatg 1560 tgtgtatcaa atattacagg actaatattg acaattgacg agggtaacgc gtctgcagaa 1620 aattatacct tcagacctgg aggaggagat atgagggaca attggagaag tgaattgtat 1680 aaatataaag tagtaaaaat tgaaccactg ggaatagcac ccaccaagac aaggagaaga 1740 gtggtggaga gagaaaaaag agcagtggga atgggagctt ctttccttgg gttcttggga 1800 gcagcaggaa gcactatggg cgcggcgtca ataacgctga cggtacaggc caggcaatta 1860 ttgtctggta tagtgcagca gcaaagcaat ttgctgagag ctatacaggc gcgacagcat 1920 atgttgcagc tcacggtctg gggcattaaa cagctccagg caagagtcct cgctgtggaa 1980 agatacctaa gggatcaaca gctcctgggg atttggggct gctctggaaa actcatctgc 2040 accactaatg tgccttggaa ctctagttgg agtaataaat cacagagtga aatctgggac 2100 aacatgactt ggatggaatg ggataaacaa attagcaatt acacagagga aatatacagg 2160 ttgcttgaag tctcgcaaac ccagcaggaa aagaatgaac aggacttatt agcattggac 2220 aaatgggcaa gtctgtggac ttggtttgac atatcacatt ggctgtggta tataaaaata 2280 ttcataatga tagtaggagg tttaataggt ttaagaataa tttttgctgt gctttctata 2340 gtaaatagag ttaggcaggg atactcacct ttgtcttttc agacccttgt cccgaaccca 2400 cggggacccg acaggcccga aggaacagaa gaaggaggtg gcgagcaaga cagagacaga 2460 tccgtgagat tagtgaacgg attcttacca gttgtctggg acgacctccg gagcctgtca 2520 ctcttcagct accgcctctt gagagactta ctcttaattg tagtgaggac tgtggaactt 2580 ctggggagaa gggggaggga agccctcaaa tatctctgga atcttctaca atactgggga 2640 caggaactaa agaatag 2657 35 243 DNA Human immunodeficiency virus type 1 isolate=90CR056; gene=vpu 35 atgtatatat taggattagg aataggagcg ctagtagtaa catttatcat agccgtaatt 60 gtgtggacca tagtatatat agaatataaa aaattggtaa ggcaaaagaa aatagacagg 120 ctaattgaaa gaataggaga aagagcagaa gacagtggca acgagagtga tggagacaca 180 gaggaattat ccaagcttat ggagatgggg caccttaatc ttgggtatgt tgctgatctg 240 tag 243 36 2538 DNA Human immunodeficiency virus type 1 isolate=90CR056; gene=env 36 atggagacac agaggaatta tccaagctta tggagatggg gcaccttaat cttgggtatg 60 ttgctgatct gtagtgctgc acaaaacttg tgggttacag tatattatgg ggtacctgtg 120 tggaaagagg caaaaaccac tctattctgt gcatcagatg ctaaggcata tgagacagaa 180 aagcataatg tctgggctac acatgcatgt gtacccacag accccaaccc acaagagatg 240 gtcatggaga atgtaacaga gagctttaat atgtgggaaa ataacatggt ggagcagatg 300 catacagaca taatcagttt atgggatcaa agcttgaaac catgtgtaaa attaacccca 360 ctctgtgtta ctctaaactg tactaatgtc agaaacaata cctctaacag cactagcagt 420 atggaggcag gaggggaact aacaaattgc tctttcaatg taactacagt actaagagat 480 aagcagcaga aagtacatgc actcttttat agacttgatg tagtaccaat tgataacaat 540 agtactcagt ataggctaat aaattgtaat acctcagtca ttacacaggc ttgcccaaag 600 gtgtcctttg aacctattcc catacattat tgtgctccag ctggctttgc gattctaaag 660 tgtaacaata aaacattcaa tggaacagga ttatgtacaa atgtcagtac agtacaatgt 720 acacatggaa ttagaccagt ggtatcaact caactgctat taaatggaag cctagcagaa 780 gaacagatca taattagaac taaaaatatc tcagacaata ccaaaaacat aatagtacag 840 cttaagacac cagtaaacat tacatgtacc aggcctaaca ataatacgag aacaagtata 900 catttagggc caggacgagc attctatgca acaggtgaca tcataggaga tataagacaa 960 gcacattgta atattagtag aacagactgg aataagactt tacaccaggt agttacacaa 1020 ttaggaatac acttgaacaa tagaacaata agctttaagc caaactcagg aggggacatg 1080 gaagttagaa cacatagttt taattgtaga ggagaatttt tctattgcaa tacatcaggg 1140 ctgtttaata gtagttggga aatgcatact aattacacat caaatgacac aaagggaaac 1200 gaaaacatta cactgccatg cagaataaaa caaattgtaa acatgtggca gagagtagga 1260 cgagcaatgt atgcccctcc catccaagga aacattatgt gtgtatcaaa tattacagga 1320 ctaatattga caattgacga gggtaacgcg tctgcagaaa attatacctt cagacctgga 1380 ggaggagata tgagggacaa ttggagaagt gaattgtata aatataaagt agtaaaaatt 1440 gaaccactgg gaatagcacc caccaagaca aggagaagag tggtggagag agaaaaaaga 1500 gcagtgggaa tgggagcttc tttccttggg ttcttgggag cagcaggaag cactatgggc 1560 gcggcgtcaa taacgctgac ggtacaggcc aggcaattat tgtctggtat agtgcagcag 1620 caaagcaatt tgctgagagc tatacaggcg cgacagcata tgttgcagct cacggtctgg 1680 ggcattaaac agctccaggc aagagtcctc gctgtggaaa gatacctaag ggatcaacag 1740 ctcctgggga tttggggctg ctctggaaaa ctcatctgca ccactaatgt gccttggaac 1800 tctagttgga gtaataaatc acagagtgaa atctgggaca acatgacttg gatggaatgg 1860 gataaacaaa ttagcaatta cacagaggaa atatacaggt tgcttgaagt ctcgcaaacc 1920 cagcaggaaa agaatgaaca ggacttatta gcattggaca aatgggcaag tctgtggact 1980 tggtttgaca tatcacattg gctgtggtat ataaaaatat tcataatgat agtaggaggt 2040 ttaataggtt taagaataat ttttgctgtg ctttctatag taaatagagt taggcaggga 2100 tactcacctt tgtcttttca gacccttgtc ccgaacccac ggggacccga caggcccgaa 2160 ggaacagaag aaggaggtgg cgagcaagac agagacagat ccgtgagatt agtgaacgga 2220 ttcttaccag ttgtctggga cgacctccgg agcctgtcac tcttcagcta ccgcctcttg 2280 agagacttac tcttaattgt agtgaggact gtggaacttc tggggagaag ggggagggaa 2340 gccctcaaat atctctggaa tcttctacaa tactggggac aggaactaaa gaatagtgct 2400 attgatttgc ttaacaccac agcaatagca gtagctgagg gaacagatgg gattatagta 2460 atagtgcaaa gagcttggag agctattctc cacataccta gaagaataag acagggcttt 2520 gaaagaagct tgctataa 2538 37 621 DNA Human immunodeficiency virus type 1 isolate=90CR056; gene=nef 37 atgggaggca aatggtcaaa aagtaggatg ggtgggtggt ctactataag ggaaagaatg 60 aggcgagctg aaccagtagc agaaggggta ggagcagtgt ctcgagattt ggatagacgc 120 ggggcagtca caattaataa tacagcatct actaatcgtg atgccgcctg gctggaagca 180 caagaggacg gggaggaagt aggctttcca gtcaggcctc aggtaccttt aagaccaatg 240 acctataagg gagcttttga tctcagccat tttttaaaag aaaagggggg actggatggg 300 ttaatttact ccaagcaaag acaggacatc cttgatttat gggtctataa cacacaaggc 360 tacttccctg actggcagaa ctacacacca gggccagggg agagatttcc cctgaccttt 420 gggtggtgct tcaagctagt accagtaaat ccacaggagg tagaacaggc caatgaagga 480 gagaacaaca gcttgctaca ccccatgagc ctgcatggaa tggaggatga cgggagagaa 540 gtgctgatgt ggaaatttga cagtcgacta gcattgacac acttggcccg agtaaagcat 600 ccggagtaca aagactgctg a 621 38 1486 DNA Human immunodeficiency virus type 1 isolate=92RW009; gene=gag 38 atgggtgcga gagcgtcaat attaagaggc ggaaaattag atgcctggga aaaaattaag 60 ttaaagccag gggggaaaga aaacatatat gatgaaacac ctagtatggg caagcaggga 120 gctggaaaga tttgcactta accctgacct tttagagaca ccagaaggct gtaaacaaat 180 aatgagacag ctgcaaccag ctcttcagac aggaacagat gaacttaggt cattatataa 240 tacagtagca accctctatt gtgtacatca aaagatagat gtaaaagaca ccaaggaggc 300 cttagacaag atagaggaag aacaaaacaa aagtcagcaa aaaacacagc aggcagaagc 360 agctgacaaa ggaaaagtca gtcaaaatta ccctatagtg caaaatgcac aagggcaaat 420 ggtacaccag gccatatcac ctagaacttt gaatgcgtgg gtaaaagtaa tagaggagaa 480 ggcttttagc caagaggtaa tacccatgtt tacagcatta tcagaaggag ccaccccaca 540 agatttaaac accatgctaa atacagtggg gggacatcaa gcagccatgc aaatgctaaa 600 agatacaatc aatgaggagg ctgcagagtg ggatagggta catccagtgc aggcagggcc 660 tgttgcgcca ggccagataa gagaaccaag gggaagtgac atagcaggaa ctactagtac 720 ccttcaggaa caaatagcat ggatgacaaa taacccacct attccagtgg gagaaattta 780 taaaagatgg ataattctgg ggttaaataa aatagtaaga atgtatagcc ctgtcagcat 840 attggacata aaacaagggc caaaggaacc ttttagagac tatgtagacc ggttctttaa 900 aaccttaaga gccgaacaag cttcacaaga tgtaaaaaat tggatgacag ataccttgtt 960 agtccaaaat gcgaacccag attgtaagac cattttaaga gcattagggc caggggcttc 1020 attagaagaa atgatgacag catgccaggg agtgggagga cccggccata aagcaagggt 1080 tttggctgaa gcaatgagcc aagtacaaca accaaacata atgatgcaga gaggcaattt 1140 taagggccag agaagaatta ttaagtgttt caactgtggc aaagaaggac acctagccag 1200 aaattgcagg gcccctagaa aaaagggctg ttggaaatgt ggaaaggagg gacaccaaat 1260 gaaagactgc actgagagac aggctaattt tttagggaaa atttggcctt ccaacaaggg 1320 gaggccagga aattttcccc agagcagact ggagccaaca gccccaccag cagagaactt 1380 tggaatgggg gaagagatag cctctcctct gaaacaggag cagaaagaca gggaaccttt 1440 aatttccctc aaatcactct ttggcaacga ccccttgtca cagtaa 1486 39 579 DNA Human immunodeficiency virus type 1 isolate=92RW009; gene=vif 39 atggaaaaca gatggcaggt gatgattgtg tggcaggtag acaggatgaa gattagaaca 60 tggaatagtc tagtaaagca ccatatgtat gcttcaagga gagctaaggg atggttttat 120 agacatcatt atgaaagcag acatccaaaa ataagttcag aagtacacat cccattaggg 180 gaagctagat tagtaataaa aacatattgg ggtttgcaaa caggggaaag agattggcat 240 ttgggtcatg gagtctccat agaatggaga ttgagaagat ataagacaca agtagaccct 300 ggcctggcag gccaactaat ccatatgcat tattttgatt gttttgcaga ctctgccata 360 aggaaagcca tattaggaca tatagttagc cctaggtgtg actatcaagc aggacataat 420 aaggtaggat ctctacaata cttggcactg acagcattga taaaaccaaa aaagataaag 480 ccacctctgc ctagtgttag taaattagta gaggataaat ggaacaagcc ccagaagacc 540 aggggccgca gagggaacca tacaatgaat ggacactag 579 40 291 DNA Human immunodeficiency virus type 1 isolate=92RW009; gene=vpr 40 atggaacaag ccccagaaga ccaggggccg cagagggaac catacaatga atggacacta 60 gagcttttag aggcactcaa gcaggaagct gtcagacact ttcctagacc atggctccat 120 gacttaggac aatatatcta tgaaacctat ggggatactt ggaggggagt agaagctata 180 ataagaattc tgcaacaact actgtttatc catttcagaa ttgggtgccg gcatagcaga 240 ataggcattt tgcaacagag aagagcaaga aatggagcca gtagatccta a 291 41 2640 DNA Human immunodeficiency virus type 1 isolate=92RW009; gene=tat 41 atggagccag tagatcctaa actagagccc tggaaccatc caggaagtca gcctaaaact 60 gcctgtaata actgttattg taaacactgt agctatcatt gtctagtttg cttccaggca 120 aaaggcttag gcatttccta tggcaggaag aagcggagac agcgacgaaa cgctcctcca 180 agcagtgaag atcatcaaaa tcctatatca aagcagtaag tagtaataaa cagtatatgt 240 aatgacttct ttagaaatct atgcaatagt agcactgata gtggcgctaa tcatagtgat 300 agttgtgtgg actttagcag gtatagaata taagaaattg ctaaagcaaa ggaaaataga 360 taggttaatt aagaaaataa gagaaagagc agaagatagt ggcaatgaga gtgatgggga 420 cattgatgaa ttatcaaaac ttgtgggggt ggggaactat gatcttgggg atgttaacaa 480 tttgtagtgc tgcaaacaac ttgtgggtta ctgtctacta tggggtacct gtgtggaaag 540 acgcagagac caccttattt tgtgcatcag atgctaaagc atatgatcca gaaaagcata 600 atgtctgggc tacacatgcc tgtgtaccca tagaccccga cccacaagaa atacatttgg 660 aaaatgtgac agaagagttt aacatgtgga aaaataacat ggtagagcag atgcatacag 720 atataatcag tctatgggac caaagcctaa agccatgtgt aaagttaacc cctctctgcg 780 ttactttaga gtgtaacaac atcaccaatg tcaacaacac tgtcaacatt acggatgaca 840 tgaaaggaga aataaaaaac tgctctttca atatgaccac agaattaagg gataagaaac 900 agagagtgta ttcacttttt tataggcttg atatagtaca aattaatagc aatagtaata 960 acagtagtca taatcagtat aggttaataa attgtaatac ctcagccatt acacaggctt 1020 gtccaaaggt atcctttgag ccaattccca taaattattg tgccccagct ggtttcgcga 1080 ttctaaagtg taaagataaa aagttcaatg gaacagggcc atgcaagaat gtcagcacag 1140 tacaatgcac acatggaatc aagccagtag tatcaactca gctgctgtta aatggcagtc 1200 tagcagaaga agagataata attagatctg aaaatattac aaacaatgcc aaaaccataa 1260 tagtacaact taacgagact gtacaaatta attgttccag acctaacaac aatacaagaa 1320 aaagtgtaca tataggacca ggacaagcat tttatgcaac aggtgacgta ataggggata 1380 taagacaagc atattgtact gtcaatggaa caaaatggaa tagaacttta caaaaggtag 1440 cagaaaaatt aagtcactac tttgagaaca ttacaacaat aatttttaag aactcctcag 1500 ggggggattt agaaattaca acacatagtt ttaattgtgg aggagaattt ttctattgta 1560 atacatcagg cttgtttaat agcacctgga gtaaaagaaa tggcacctgg cagtcaaatg 1620 gcacagaatt aaatataaca ctcccatgca gaataaagca aattataaat atgtggcaga 1680 ggacaggaca agcaatgtat gcccctccca tccaaggagt aataagctgt gtatcaaaca 1740 ttacaggact actattaaca agagatggtg gaaataataa tactacaact gaaaccttca 1800 gacctggagg aggagatatg agggataatt ggagaagtga actatataaa tataaagtag 1860 taaaaattga accactagga gtagcaccca ccagggcaaa gaggagagtg gtggagagag 1920 aaaaaagagc agttggactg ggagctgtct tcattgggtt cttaggagca gcaggaagca 1980 ctatgggcgc ggcgtcaata acgctgacgg tacaggccag acaattattg tctggcatag 2040 tgcaacagca aagcaatttg ctgagggcta tagaggctca acagcatcta ttaaaactca 2100 cagtctgggg cattaaacag ctccaggcaa gagtcctggc tctggaaaga tacctaaggg 2160 atcaacagct cctaggaatt tggggctgct ctggaaaact catctgcacc actaatgtgc 2220 cctggaactc tagttggagt aataagactc agcaggaaat atgggataac atgacctggc 2280 agcaatggga taaagaaatt ggcaattaca cacaaataat atatagtcta attgaagaat 2340 cgcagaacca gcaggaaaag aatgaacaag acttattggc attggacaag tgggcaaatc 2400 tgtggaattg gtttgacata tcaaattggc tgtggtatat aaaaatattc ataatgatag 2460 taggaggctt aataggttta agaataattt ttgctgtgct ctctatagtg aacagagtta 2520 ggcagggata ctcaccatta tcgtttcaga cccttatccc aaacccgagg ggacccgaca 2580 ggctcggagg aatcgaagaa gaaggtggag agcaagacag aggcagatcc attcgattag 2640 42 2658 DNA Human immunodeficiency virus type 1 isolate=92RW009; gene=rev 42 atggcaggaa gaagcggaga cagcgacgaa acgctcctcc aagcagtgaa gatcatcaaa 60 atcctatatc aaagcagtaa gtagtaataa acagtatatg taatgacttc tttagaaatc 120 tatgcaatag tagcactgat agtggcgcta atcatagtga tagttgtgtg gactttagca 180 ggtatagaat ataagaaatt gctaaagcaa aggaaaatag ataggttaat taagaaaata 240 agagaaagag cagaagatag tggcaatgag agtgatgggg acattgatga attatcaaaa 300 cttgtggggg tggggaacta tgatcttggg gatgttaaca atttgtagtg ctgcaaacaa 360 cttgtgggtt actgtctact atggggtacc tgtgtggaaa gacgcagaga ccaccttatt 420 ttgtgcatca gatgctaaag catatgatcc agaaaagcat aatgtctggg ctacacatgc 480 ctgtgtaccc atagaccccg acccacaaga aatacatttg gaaaatgtga cagaagagtt 540 taacatgtgg aaaaataaca tggtagagca gatgcataca gatataatca gtctatggga 600 ccaaagccta aagccatgtg taaagttaac ccctctctgc gttactttag agtgtaacaa 660 catcaccaat gtcaacaaca ctgtcaacat tacggatgac atgaaaggag aaataaaaaa 720 ctgctctttc aatatgacca cagaattaag ggataagaaa cagagagtgt attcactttt 780 ttataggctt gatatagtac aaattaatag caatagtaat aacagtagtc ataatcagta 840 taggttaata aattgtaata cctcagccat tacacaggct tgtccaaagg tatcctttga 900 gccaattccc ataaattatt gtgccccagc tggtttcgcg attctaaagt gtaaagataa 960 aaagttcaat ggaacagggc catgcaagaa tgtcagcaca gtacaatgca cacatggaat 1020 caagccagta gtatcaactc agctgctgtt aaatggcagt ctagcagaag aagagataat 1080 aattagatct gaaaatatta caaacaatgc caaaaccata atagtacaac ttaacgagac 1140 tgtacaaatt aattgttcca gacctaacaa caatacaaga aaaagtgtac atataggacc 1200 aggacaagca ttttatgcaa caggtgacgt aataggggat ataagacaag catattgtac 1260 tgtcaatgga acaaaatgga atagaacttt acaaaaggta gcagaaaaat taagtcacta 1320 ctttgagaac attacaacaa taatttttaa gaactcctca gggggggatt tagaaattac 1380 aacacatagt tttaattgtg gaggagaatt tttctattgt aatacatcag gcttgtttaa 1440 tagcacctgg agtaaaagaa atggcacctg gcagtcaaat ggcacagaat taaatataac 1500 actcccatgc agaataaagc aaattataaa tatgtggcag aggacaggac aagcaatgta 1560 tgcccctccc atccaaggag taataagctg tgtatcaaac attacaggac tactattaac 1620 aagagatggt ggaaataata atactacaac tgaaaccttc agacctggag gaggagatat 1680 gagggataat tggagaagtg aactatataa atataaagta gtaaaaattg aaccactagg 1740 agtagcaccc accagggcaa agaggagagt ggtggagaga gaaaaaagag cagttggact 1800 gggagctgtc ttcattgggt tcttaggagc agcaggaagc actatgggcg cggcgtcaat 1860 aacgctgacg gtacaggcca gacaattatt gtctggcata gtgcaacagc aaagcaattt 1920 gctgagggct atagaggctc aacagcatct attaaaactc acagtctggg gcattaaaca 1980 gctccaggca agagtcctgg ctctggaaag atacctaagg gatcaacagc tcctaggaat 2040 ttggggctgc tctggaaaac tcatctgcac cactaatgtg ccctggaact ctagttggag 2100 taataagact cagcaggaaa tatgggataa catgacctgg cagcaatggg ataaagaaat 2160 tggcaattac acacaaataa tatatagtct aattgaagaa tcgcagaacc agcaggaaaa 2220 gaatgaacaa gacttattgg cattggacaa gtgggcaaat ctgtggaatt ggtttgacat 2280 atcaaattgg ctgtggtata taaaaatatt cataatgata gtaggaggct taataggttt 2340 aagaataatt tttgctgtgc tctctatagt gaacagagtt aggcagggat actcaccatt 2400 atcgtttcag acccttatcc caaacccgag gggacccgac aggctcggag gaatcgaaga 2460 agaaggtgga gagcaagaca gaggcagatc cattcgatta gtgagcggat tcttagcact 2520 tgcctgggac gacctacgga gcctgtgcct tttcagctac caccgattga gagacttact 2580 attgattgca gcgaggacgg tggaacttct gggacgcagc agtctcaggg gactacagag 2640 ggggtgggaa acccttaa 2658 43 246 DNA Human immunodeficiency virus type 1 isolate=92RW009; gene=vpu 43 atgacttctt tagaaatcta tgcaatagta gcactgatag tggcgctaat catagtgata 60 gttgtgtgga ctttagcagg tatagaatat aagaaattgc taaagcaaag gaaaatagat 120 aggttaatta agaaaataag agaaagagca gaagatagtg gcaatgagag tgatggggac 180 attgatgaat tatcaaaact tgtgggggtg gggaactatg atcttgggga tgttaacaat 240 ttgtag 246 44 2583 DNA Human immunodeficiency virus type 1 isolate=92RW009; gene=env 44 atgagagtga tggggacatt gatgaattat caaaacttgt gggggtgggg aactatgatc 60 ttggggatgt taacaatttg tagtgctgca aacaacttgt gggttactgt ctactatggg 120 gtacctgtgt ggaaagacgc agagaccacc ttattttgtg catcagatgc taaagcatat 180 gatccagaaa agcataatgt ctgggctaca catgcctgtg tacccataga ccccgaccca 240 caagaaatac atttggaaaa tgtgacagaa gagtttaaca tgtggaaaaa taacatggta 300 gagcagatgc atacagatat aatcagtcta tgggaccaaa gcctaaagcc atgtgtaaag 360 ttaacccctc tctgcgttac tttagagtgt aacaacatca ccaatgtcaa caacactgtc 420 aacattacgg atgacatgaa aggagaaata aaaaactgct ctttcaatat gaccacagaa 480 ttaagggata agaaacagag agtgtattca cttttttata ggcttgatat agtacaaatt 540 aatagcaata gtaataacag tagtcataat cagtataggt taataaattg taatacctca 600 gccattacac aggcttgtcc aaaggtatcc tttgagccaa ttcccataaa ttattgtgcc 660 ccagctggtt tcgcgattct aaagtgtaaa gataaaaagt tcaatggaac agggccatgc 720 aagaatgtca gcacagtaca atgcacacat ggaatcaagc cagtagtatc aactcagctg 780 ctgttaaatg gcagtctagc agaagaagag ataataatta gatctgaaaa tattacaaac 840 aatgccaaaa ccataatagt acaacttaac gagactgtac aaattaattg ttccagacct 900 aacaacaata caagaaaaag tgtacatata ggaccaggac aagcatttta tgcaacaggt 960 gacgtaatag gggatataag acaagcatat tgtactgtca atggaacaaa atggaataga 1020 actttacaaa aggtagcaga aaaattaagt cactactttg agaacattac aacaataatt 1080 tttaagaact cctcaggggg ggatttagaa attacaacac atagttttaa ttgtggagga 1140 gaatttttct attgtaatac atcaggcttg tttaatagca cctggagtaa aagaaatggc 1200 acctggcagt caaatggcac agaattaaat ataacactcc catgcagaat aaagcaaatt 1260 ataaatatgt ggcagaggac aggacaagca atgtatgccc ctcccatcca aggagtaata 1320 agctgtgtat caaacattac aggactacta ttaacaagag atggtggaaa taataatact 1380 acaactgaaa ccttcagacc tggaggagga gatatgaggg ataattggag aagtgaacta 1440 tataaatata aagtagtaaa aattgaacca ctaggagtag cacccaccag ggcaaagagg 1500 agagtggtgg agagagaaaa aagagcagtt ggactgggag ctgtcttcat tgggttctta 1560 ggagcagcag gaagcactat gggcgcggcg tcaataacgc tgacggtaca ggccagacaa 1620 ttattgtctg gcatagtgca acagcaaagc aatttgctga gggctataga ggctcaacag 1680 catctattaa aactcacagt ctggggcatt aaacagctcc aggcaagagt cctggctctg 1740 gaaagatacc taagggatca acagctccta ggaatttggg gctgctctgg aaaactcatc 1800 tgcaccacta atgtgccctg gaactctagt tggagtaata agactcagca ggaaatatgg 1860 gataacatga cctggcagca atgggataaa gaaattggca attacacaca aataatatat 1920 agtctaattg aagaatcgca gaaccagcag gaaaagaatg aacaagactt attggcattg 1980 gacaagtggg caaatctgtg gaattggttt gacatatcaa attggctgtg gtatataaaa 2040 atattcataa tgatagtagg aggcttaata ggtttaagaa taatttttgc tgtgctctct 2100 atagtgaaca gagttaggca gggatactca ccattatcgt ttcagaccct tatcccaaac 2160 ccgaggggac ccgacaggct cggaggaatc gaagaagaag gtggagagca agacagaggc 2220 agatccattc gattagtgag cggattctta gcacttgcct gggacgacct acggagcctg 2280 tgccttttca gctaccaccg attgagagac ttactattga ttgcagcgag gacggtggaa 2340 cttctgggac gcagcagtct caggggacta cagagggggt gggaaaccct taagtatcta 2400 ggaaatcttg tgcagtattg gggtctggaa ctaaaaagga gtgctattaa tctgcttgat 2460 accacagcaa tagtagtagc tgaaggaaca gataggatta tagaattaat acaaagaatt 2520 agcagagcta tctataacat acctagcaga ataagacagg gctttgaagc agctttgcaa 2580 taa 2583 45 624 DNA Human immunodeficiency virus type 1 isolate=92RW009; gene=nef 45 atgggaagca agtggtcaaa atgtagtcca gtaggatggc ctgctgtaag agaaagacta 60 aggcaaactg agccagcagc agagggagta ggagcagcgt ctcaagacct agacaaatat 120 ggggcactta caagtagcaa cacacccagc aacaatgctg attgtgcctg gctggcagca 180 caagaggagg aaaacgaagt aggctttcca gtcagacctc aggtgccttt aagaccaatg 240 acttataaag cagcagttga tctcagcttc tttttaaaag aaaagggggg actggaaggg 300 ttaatttact ctaagaaaag gcaagacatc ctggatttgt gggtctataa cacacaaggc 360 tacttccctg attggcaaaa ctacacacca ggaccagggg tcagatatcc actgactttt 420 ggatggtgtt acaagctagt gccagttgac ccaagggaag tggaagaagc caatgaagga 480 gaggacaact gcttactaca ccctctgagc cagcatggaa tggaggatga ggacagagaa 540 gtcttaaagt ggaagtttga cagtcaccta gcacacagac acatggcccg cgagctacat 600 ccggagtatt ataaagactg ctga 624 46 8 DNA Human immunodeficiency virus type 1 isolate=92RW009; standard name=3′ LTR repeat region; note=3′ R repeat should end one base beyond end of this 46 aaaaaaaa 8 47 1494 DNA Human immunodeficiency virus type 1 isolate=92NG003; gene=gag 47 atgggtgcga gagcgtcagt attaagcggg ggaaaattag atgcatggga aaaaattcgg 60 ttgaggccag ggggaaagaa aaaatataga atgaaacatt tagtatgggc aagcagggaa 120 ctggagagat ttgcacttaa ccctgacctc ttagaaacaa cagaaggttg tcagcaaata 180 atgagacagc tgcaaccatc tctccagaca ggaacagagg agattaaatc attatttaat 240 acagtagcaa ccctctattg tgtacatcaa aggatagagg taaaagacac caaagaagct 300 ctagaggaag tggaaaaaat acaaaagaac agtcagcaag aaacacagaa ggcagcaatg 360 ggtaaaggaa acagcagcca agttagccaa aattatccta tagtgcagaa tgcacaaggg 420 caagtggtac accagcccat atcacctagg actttaaatg catgggtaaa agtaatagaa 480 gaaaagaact tcagtccaga agtaataccc atgtttacag cattatcaga aggagccacc 540 ccacaagatt tgaataccat gctaaacacc gtgggggggc atcaagcagc tatgcaaatg 600 ctaaaagatt ctattaatga agaagctgca gagtgggata ggctacatcc acaacaggca 660 ggacctattc caccaggcca gataagagaa ccaaggggaa gtgatatagc aggaactact 720 agtaccctgc aggaacaaat aacatggatg accagcaacc cacctatccc agtgggagaa 780 atttataaaa gatggataat tctggggtta aataaaatag tgagaatgta tagccctgtc 840 agtattttag acataaaaca agggccaaaa gaacccttca gagattatgt ggataggttc 900 tttaaaactt tgagagctga gcaagccaca caggaggtaa aaaactggat gacagacacc 960 ttgttggtcc aaaatgcgaa cccagattgt aagaccatcc taagagcatt aggagcagga 1020 gctacactag aagaaatgtt gacagcatgt caaggagtgg gaggacccag ccacaaagca 1080 agagttttag ctgaggcaat gagccgggca acaggtacat cagcagccat aatgatgcag 1140 aaaaacaatt ttaagggccc gagaagaggt attaagtgtt tcaactgtgg caaggaagga 1200 catctagcca gaaattgcag ggcccctagg aaaaaaggct gttggaaatg tggaaaggag 1260 ggacatcaaa tgaaagactg cacagagaga caggctaatt ttttagggaa aatttggcct 1320 tccaacaagg ggaggccagg gaattttctt cagaacaggc cagagccaac agccccaccc 1380 gcagagagct tcgggttcgg agaggagata gccccttccc tgaagcagga gccgagggaa 1440 aaggaatcac ctccattaac ctccctcaaa tcactctttg gcaacgaccc ctag 1494 48 4307 DNA Human immunodeficiency virus type 1 isolate=92NG003; gene=gag-pol fusion 48 atgggtgcga gagcgtcagt attaagcggg ggaaaattag atgcatggga aaaaattcgg 60 ttgaggccag ggggaaagaa aaaatataga atgaaacatt tagtatgggc aagcagggaa 120 ctggagagat ttgcacttaa ccctgacctc ttagaaacaa cagaaggttg tcagcaaata 180 atgagacagc tgcaaccatc tctccagaca ggaacagagg agattaaatc attatttaat 240 acagtagcaa ccctctattg tgtacatcaa aggatagagg taaaagacac caaagaagct 300 ctagaggaag tggaaaaaat acaaaagaac agtcagcaag aaacacagaa ggcagcaatg 360 ggtaaaggaa acagcagcca agttagccaa aattatccta tagtgcagaa tgcacaaggg 420 caagtggtac accagcccat atcacctagg actttaaatg catgggtaaa agtaatagaa 480 gaaaagaact tcagtccaga agtaataccc atgtttacag cattatcaga aggagccacc 540 ccacaagatt tgaataccat gctaaacacc gtgggggggc atcaagcagc tatgcaaatg 600 ctaaaagatt ctattaatga agaagctgca gagtgggata ggctacatcc acaacaggca 660 ggacctattc caccaggcca gataagagaa ccaaggggaa gtgatatagc aggaactact 720 agtaccctgc aggaacaaat aacatggatg accagcaacc cacctatccc agtgggagaa 780 atttataaaa gatggataat tctggggtta aataaaatag tgagaatgta tagccctgtc 840 agtattttag acataaaaca agggccaaaa gaacccttca gagattatgt ggataggttc 900 tttaaaactt tgagagctga gcaagccaca caggaggtaa aaaactggat gacagacacc 960 ttgttggtcc aaaatgcgaa cccagattgt aagaccatcc taagagcatt aggagcagga 1020 gctacactag aagaaatgtt gacagcatgt caaggagtgg gaggacccag ccacaaagca 1080 agagttttag ctgaggcaat gagccgggca acaggtacat cagcagccat aatgatgcag 1140 aaaaacaatt ttaagggccc gagaagaggt attaagtgtt tcaactgtgg caaggaagga 1200 catctagcca gaaattgcag ggcccctagg aaaaaaggct gttggaaatg tggaaaggag 1260 ggacatcaaa tgaaagactg cacagagaga caggctaatt ttttagggaa aatttggcct 1320 tccaacaagg ggaggccagg gaattttctt cagaacaggc cagagccaac agccccaccc 1380 gcagagagct tcgggttcgg agaggagata gccccttccc tgaagcagga gccgagggaa 1440 aaggaatcac ctccattaac ctccctcaaa tcactctttg gcaacgaccc ctagtcacag 1500 taagaatagg gggacagcta atagaagctc tattagacac aggagcagat gatacagtat 1560 tagaacaaat aaatttacca ggaaaatgga aaccaaaaat gataggggga attggaggat 1620 ttatcaaagt aaaacagtat gatcaaatac ttatagaaat tgaagggaaa aaggctatag 1680 ggacagtact agtaggacct acacctatca acataattgg gagaaatatg ttgactcaaa 1740 ttggttgtac tttaaatttt ccaattagtc ctattgagac tgtaccagta aaattaaaac 1800 caggaataga tggcccaaag gttaaacaat ggccattgac agaagagaaa ataaaagcat 1860 taacagaaat ttgtacagat atggaaaagg aaggaaaaat ttcaaaaatt gggccagaaa 1920 atccatacaa cactccaata tttgccataa agaaaaaaga cagtactaaa tggagaaagt 1980 tggtagattt cagagagctc aataaaagaa ctcaagactt ctgggaggtc caattaggca 2040 tacctcatcc cgcggggtta aaaaagaaaa gatcagtaac agtactagat gtgggggatg 2100 catatttttc aattccccta gatgaaaact ttagaaagta tacagcattc actataccta 2160 gtataaataa tgagacacca gggattagat atcagtacaa tgtgcttccg caaggatgga 2220 aaggatcacc agcaatattt cagagtagca tgacaaaaat cttagaaccc tttagaacag 2280 aaaatccaga aatagtgatc tatcagtaca tggatgattt atatgtagga tctgacttag 2340 aaacagggca gcatagagca aaaatagagg aattaagaaa tcatctactg agatggggat 2400 ttaccacacc agataaaaaa catcagaaag aacctccatt tctctggatg ggatatgagc 2460 tccatcctga caaatggacg gtacaaccta tacagctgcc aaacaaagaa agctggactg 2520 tcaatgatat acaaaaatta gtgggaaaac taaattgggc aagtcagatt tatccaggga 2580 ttaaagtaaa gcaactatgt aaactcctta ggggggccaa agcactaaca gacatagtac 2640 cactgactga agaagcagaa ttagaattgg cagagaacag ggaaattcta aaagaacctg 2700 tacatggagt ctactatgac ccatcaaaag aattaatagc agaattacag aaacaagggt 2760 gcgaccaatg gacatatcaa atttatcaag agccatacaa aaatctgaaa acaggaaagt 2820 atgcaaaaag ggggtctgcc cacactaatg atgtaaaaca gttaacagaa gcagtgcaaa 2880 aaatagccac agagagcata gtaatatggg gaaaagttcc taaatttaaa ctacctataa 2940 ggaaagaaac atgggaagta tggtggacag aatattggca ggccacctgg attcctgatt 3000 gggagtttgt caatacccct cctctagtaa agttatggta tcgattagaa acagaaccca 3060 taccaggagc agaaacttac tatgtagatg gggcagctaa taaagaaaca aaattaggaa 3120 aggcaggata tgttactgac agaggaaaac aaaaaattat caccatacag gaaacaacaa 3180 atcaaaaaac tgaattacac gcaattcagc tagctttgca ggattcagga tcagaagtaa 3240 acatagtaac agactcacag tatgcattag gaatcattca agcacaacca gataggagtg 3300 aatcagaatt agtcaatcaa ataatagaac agctaataaa aaaggaaaag gtctacttaa 3360 catgggtacc agcacacaaa ggaattgggg gaaatgaaca agtagataaa ttagtcagta 3420 gtggaatcag aaaagtactg tttttagatg gcatagacaa agctcaagag gaccatgaaa 3480 gatatcacag caattggaga gcaatggcta gtgattttaa tctgccacct atagtagcaa 3540 aagaaatagt ggccagctgt gataaatgtc agctaaaagg ggaagccatg catggacaag 3600 tagactgtag tccaggaata tggcaattag attgcacaca tctagaagga aaagtcatta 3660 tagtagcagt ccatgtagcc agtggctata tagaagcaga agttatccca gcagaaacag 3720 gacaggagac agcatacttc ctgctaaaat tagcaggaag atggccagta aaagtaatac 3780 acacagacaa tggcagcaat ttcaccagtg ctgcaatgaa agcagcctgt tggtgggcaa 3840 atatccaaca ggaatttgga attccctaca atccccaaag ccaaggagta gtggaatcta 3900 tgaataaaga attaaagaaa attatagggc aggtcaggga tcaagctgaa cacctcaaga 3960 cagcagtaca gatggcagta ttcattcaca attttaaaag aaaagggggg attggggggt 4020 acagtgcagg ggaaagaata atagacataa tagcatcaga tatacaaact aaagaactac 4080 aaaaacagat tataaaaatt caaaattttc gggtctatta cagggacagc agagacccca 4140 tttggaaagg accagcaaaa ctactctgga aaggtgaagg ggcagtagta atacaggaca 4200 atagtgagat aaaggtagta ccaagaagaa aagtaaaaat cattaaggat tatggaaaac 4260 agatggcagg tggtgattgt gtggcaggta gacaggatga ggattag 4307 49 579 DNA Human immunodeficiency virus type 1 isolate=92NG003; gene=vif 49 atggaaaaca gatggcaggt ggtgattgtg tggcaggtag acaggatgag gattagaaca 60 tggaacagtt tagtaaaata tcatatgtat aaatctaaga aagctaagga ttggttttat 120 agacatcact atgaaagtag gcatccaaaa gtaagttcag aagtacacat cccactaggg 180 gaggctagat tagtagtaag aacatattgg ggtctgcata caggagaaag agactggcac 240 ttgggtcagg gggtctccat agaatggaag cagagaagat atagcacaca aatagatcct 300 gacctagcag accaactgat tcacctgcat tattttaact gtttttcaga atcggccgta 360 aggaaagcca tactaggaga agtagttaga cctaggtgtg aatatcaaac aggacataat 420 caggtaggat cactacaata tttagcactc aaagcattag taacaccaac acagacaaag 480 ccacctttac ctagtgttaa gaagttaaca gaagatagat ggaacgagcc ccagaagacc 540 aggggccaca gagggagcca ttcaacgaat ggacactag 579 50 114 DNA Human immunodeficiency virus type 1 isolate=92NG003; gene=vpr 50 atggaacgag ccccagaaga ccaggggcca cagagggagc cattcaacga atggacacta 60 gaactgttag aagaacttaa acatgaagct gttagacatg gcttcatgga ttag 114 51 2579 DNA Human immunodeficiency virus type 1 isolate=92NG003; gene=tat 51 atggagctgg tagatcctag cctagagccc tggaaccacc caggaagtca gcctacaact 60 gcttgtaaca aatgttactg taaaatatgc tgctggcatt gccaattgtg ctttctgaac 120 aagggcttag gcatctccta tggcaggaag aagcggagac gccgacgagg aactcctcag 180 agtcaccagg atcatcaaaa tcctgtacca aagcagtgag tagtaatagt tagtatatgt 240 gatgcaatcc ttagaaatag ctgcaatagc aggactagta gtagcagcca tagcagccat 300 agttgtgtgg accatagaaa aataaagaaa caggagaaaa tagacaggtt acttgataga 360 ataagagaaa gagcagaaga tagtggcaat gagagtgaag gggacacaga ggaattggca 420 acacttgtgg acatggtgga ctttgatcct tgggttggtg ataatttgta gtgcctcaaa 480 taacttgtgg gtcacagtct attatggggt accagtgtgg gaagacgcag atacccctct 540 attttgtgca tctgatgcta aagcatatag tactgaaaga cataatgtct gggccacaca 600 tgcctgtgta cccacagacc ccaacccaca agagataact ctggaaaatg taacagaaac 660 ttttaacatg tggaaaaata acatggtaga acagatgcat gaggatataa tcagtttatg 720 ggatgaaagc ctaaagccat gtgtaaagct aacccctctc tgtgttacct taaactgtac 780 taatgtcaat tgtaacagta atgtgaccag cactgggaac agtgctggga ccaacgctac 840 gtgtaacata gaagaagcaa acaacttaaa aaactgctct ttcaatataa ccacagaaat 900 aagagataag aaaaagacag aatatgcgct tttctataga cttgatgtgg taccaatcga 960 tggtaataat aatgtctcaa ataactatag gctaataaat tgtaatgtct caaccattaa 1020 acaagcttgt ccaaaggtgt cttttgaccc acttcccata cattattgtg ctccagctgg 1080 gtttgcgatt ttaaagtgta ggggtaagaa tttcactgga acaggacaat gtaaaaatgt 1140 cagttcagta caatgtacac atggaattaa accagtggta tcaactcaat tactactaaa 1200 tggtagtcta gcagaaggag aaatagtaat tagatctgaa aacctcacag acaatgccaa 1260 agtcataata gtacagctta ataaaactat aggaattaat tgtaccagac ccaacaacaa 1320 tacaagaaaa agtataagaa tcggacctgg acaagcgttc tatgcaacag gtgaaataat 1380 aggacaagaa tggcaggaga tgttacagaa ggtacaggca caactagaac aggtctttaa 1440 caaaagtata acctttaact catccgcagg aggggaccta gaaattacaa cacatagttt 1500 taattgtaga ggagaatttt tctattgtaa tacatcagga ttgtttaatg aatcaggagg 1560 gaatgatacc actatcacac tcccatgtaa gataaaacaa attgtgagaa tgtggcagag 1620 agtgggacaa gcaatgtatg cccctcccat cgcaggagat attacatgta gatcaaacat 1680 tacagggcta ttattaacaa gagatggtgg ggttaataat actggaaatg agaccttcag 1740 acctggagga ggagatatga gggacaattg gagaagtgaa ttatataagt ataaaatagt 1800 aaaaattaaa ccactaggaa tagcacccac caaggcaagg agaagagtgg tggagagagg 1860 aaaaagggca gttggactgg gagctgtctt ccttgggttc ttaggagcag caggaagcac 1920 tatgggcgcg gggtcaataa cgctgacggt acaggtcaga caattattgt ctggcatagt 1980 gcaacagcaa agcaatttgc tgagggctat agaggcgcag caacatctat tgcaactcac 2040 agtctggggc attaaacagc tccaggcaag agtcctggct gtagaaagat acctaaagga 2100 tcaacagctc ctagggattt ggggctgctc tggaaaactc atctgcacca ctaatgtgcc 2160 ttggaacact agttggagta ataaatctta tgaggagatt tgggataaca tgacctggat 2220 acaatgggaa agggaagtca gcaattacac acaacaaata tacagcctaa ttgaagaatc 2280 gcagaaccag caggaaaaga atgaacaaga cttattggca ttggacaagt gggcaagttt 2340 gtggaactgg tttgacataa caaaatggct atggtatata aaaatattta taatgatagt 2400 aggaggttta ataggtttaa gaatagtttt tgctgtgctt tctatagtaa atagagttag 2460 gcagggatac tcacctttgt cattccagac ccttacccac caccagaggg aacccgacag 2520 gcccgaaaga atcgaagaag gaggtggaga gcaagacaga gacagatcag tgcgcttag 2579 52 2645 DNA Human immunodeficiency virus type 1 isolate=92NG003; gene=rev 52 atggcaggaa gaagcggaga cgccgacgag gaactcctca gagtcaccag gatcatcaaa 60 atcctgtacc aaagcagtga gtagtaatag ttagtatatg tgatgcaatc cttagaaata 120 gctgcaatag caggactagt agtagcagcc atagcagcca tagttgtgtg gaccatagaa 180 aaataaagaa acaggagaaa atagacaggt tacttgatag aataagagaa agagcagaag 240 atagtggcaa tgagagtgaa ggggacacag aggaattggc aacacttgtg gacatggtgg 300 actttgatcc ttgggttggt gataatttgt agtgcctcaa ataacttgtg ggtcacagtc 360 tattatgggg taccagtgtg ggaagacgca gatacccctc tattttgtgc atctgatgct 420 aaagcatata gtactgaaag acataatgtc tgggccacac atgcctgtgt acccacagac 480 cccaacccac aagagataac tctggaaaat gtaacagaaa cttttaacat gtggaaaaat 540 aacatggtag aacagatgca tgaggatata atcagtttat gggatgaaag cctaaagcca 600 tgtgtaaagc taacccctct ctgtgttacc ttaaactgta ctaatgtcaa ttgtaacagt 660 aatgtgacca gcactgggaa cagtgctggg accaacgcta cgtgtaacat agaagaagca 720 aacaacttaa aaaactgctc tttcaatata accacagaaa taagagataa gaaaaagaca 780 gaatatgcgc ttttctatag acttgatgtg gtaccaatcg atggtaataa taatgtctca 840 aataactata ggctaataaa ttgtaatgtc tcaaccatta aacaagcttg tccaaaggtg 900 tcttttgacc cacttcccat acattattgt gctccagctg ggtttgcgat tttaaagtgt 960 aggggtaaga atttcactgg aacaggacaa tgtaaaaatg tcagttcagt acaatgtaca 1020 catggaatta aaccagtggt atcaactcaa ttactactaa atggtagtct agcagaagga 1080 gaaatagtaa ttagatctga aaacctcaca gacaatgcca aagtcataat agtacagctt 1140 aataaaacta taggaattaa ttgtaccaga cccaacaaca atacaagaaa aagtataaga 1200 atcggacctg gacaagcgtt ctatgcaaca ggtgaaataa taggacaaga atggcaggag 1260 atgttacaga aggtacaggc acaactagaa caggtcttta acaaaagtat aacctttaac 1320 tcatccgcag gaggggacct agaaattaca acacatagtt ttaattgtag aggagaattt 1380 ttctattgta atacatcagg attgtttaat gaatcaggag ggaatgatac cactatcaca 1440 ctcccatgta agataaaaca aattgtgaga atgtggcaga gagtgggaca agcaatgtat 1500 gcccctccca tcgcaggaga tattacatgt agatcaaaca ttacagggct attattaaca 1560 agagatggtg gggttaataa tactggaaat gagaccttca gacctggagg aggagatatg 1620 agggacaatt ggagaagtga attatataag tataaaatag taaaaattaa accactagga 1680 atagcaccca ccaaggcaag gagaagagtg gtggagagag gaaaaagggc agttggactg 1740 ggagctgtct tccttgggtt cttaggagca gcaggaagca ctatgggcgc ggggtcaata 1800 acgctgacgg tacaggtcag acaattattg tctggcatag tgcaacagca aagcaatttg 1860 ctgagggcta tagaggcgca gcaacatcta ttgcaactca cagtctgggg cattaaacag 1920 ctccaggcaa gagtcctggc tgtagaaaga tacctaaagg atcaacagct cctagggatt 1980 tggggctgct ctggaaaact catctgcacc actaatgtgc cttggaacac tagttggagt 2040 aataaatctt atgaggagat ttgggataac atgacctgga tacaatggga aagggaagtc 2100 agcaattaca cacaacaaat atacagccta attgaagaat cgcagaacca gcaggaaaag 2160 aatgaacaag acttattggc attggacaag tgggcaagtt tgtggaactg gtttgacata 2220 acaaaatggc tatggtatat aaaaatattt ataatgatag taggaggttt aataggttta 2280 agaatagttt ttgctgtgct ttctatagta aatagagtta ggcagggata ctcacctttg 2340 tcattccaga cccttaccca ccaccagagg gaacccgaca ggcccgaaag aatcgaagaa 2400 ggaggtggag agcaagacag agacagatca gtgcgcttag tgagcggatt cttagcactt 2460 gcctgggacg acctgcggaa cctgtgcctc ttcagctacc accgattgag agacttagtc 2520 ttgattgcag cgaggacagc agaactcctg agacgcagca gtctccaggg actgagactg 2580 gggtgggagg gcctcaaata tctgtggaat ctcctgttgt attggggtcg ggaactaaag 2640 aatag 2645 53 230 DNA Human immunodeficiency virus type 1 isolate=92NG003; gene=vpu 53 atgcaatcct tagaaatagc tgcaatagca ggactagtag tagcagccat agcagccata 60 gttgtgtgga ccatagaaaa ataaagaaac aggagaaaat agacaggtta cttgatagaa 120 taagagaaag agcagaagat agtggcaatg agagtgaagg ggacacagag gaattggcaa 180 cacttgtgga catggtggac tttgatcctt gggttggtga taatttgtag 230 54 2538 DNA Human immunodeficiency virus type 1 isolate=92NG003; gene=env 54 atgagagtga aggggacaca gaggaattgg caacacttgt ggacatggtg gactttgatc 60 cttgggttgg tgataatttg tagtgcctca aataacttgt gggtcacagt ctattatggg 120 gtaccagtgt gggaagacgc agatacccct ctattttgtg catctgatgc taaagcatat 180 agtactgaaa gacataatgt ctgggccaca catgcctgtg tacccacaga ccccaaccca 240 caagagataa ctctggaaaa tgtaacagaa acttttaaca tgtggaaaaa taacatggta 300 gaacagatgc atgaggatat aatcagttta tgggatgaaa gcctaaagcc atgtgtaaag 360 ctaacccctc tctgtgttac cttaaactgt actaatgtca attgtaacag taatgtgacc 420 agcactggga acagtgctgg gaccaacgct acgtgtaaca tagaagaagc aaacaactta 480 aaaaactgct ctttcaatat aaccacagaa ataagagata agaaaaagac agaatatgcg 540 cttttctata gacttgatgt ggtaccaatc gatggtaata ataatgtctc aaataactat 600 aggctaataa attgtaatgt ctcaaccatt aaacaagctt gtccaaaggt gtcttttgac 660 ccacttccca tacattattg tgctccagct gggtttgcga ttttaaagtg taggggtaag 720 aatttcactg gaacaggaca atgtaaaaat gtcagttcag tacaatgtac acatggaatt 780 aaaccagtgg tatcaactca attactacta aatggtagtc tagcagaagg agaaatagta 840 attagatctg aaaacctcac agacaatgcc aaagtcataa tagtacagct taataaaact 900 ataggaatta attgtaccag acccaacaac aatacaagaa aaagtataag aatcggacct 960 ggacaagcgt tctatgcaac aggtgaaata ataggacaag aatggcagga gatgttacag 1020 aaggtacagg cacaactaga acaggtcttt aacaaaagta taacctttaa ctcatccgca 1080 ggaggggacc tagaaattac aacacatagt tttaattgta gaggagaatt tttctattgt 1140 aatacatcag gattgtttaa tgaatcagga gggaatgata ccactatcac actcccatgt 1200 aagataaaac aaattgtgag aatgtggcag agagtgggac aagcaatgta tgcccctccc 1260 atcgcaggag atattacatg tagatcaaac attacagggc tattattaac aagagatggt 1320 ggggttaata atactggaaa tgagaccttc agacctggag gaggagatat gagggacaat 1380 tggagaagtg aattatataa gtataaaata gtaaaaatta aaccactagg aatagcaccc 1440 accaaggcaa ggagaagagt ggtggagaga ggaaaaaggg cagttggact gggagctgtc 1500 ttccttgggt tcttaggagc agcaggaagc actatgggcg cggggtcaat aacgctgacg 1560 gtacaggtca gacaattatt gtctggcata gtgcaacagc aaagcaattt gctgagggct 1620 atagaggcgc agcaacatct attgcaactc acagtctggg gcattaaaca gctccaggca 1680 agagtcctgg ctgtagaaag atacctaaag gatcaacagc tcctagggat ttggggctgc 1740 tctggaaaac tcatctgcac cactaatgtg ccttggaaca ctagttggag taataaatct 1800 tatgaggaga tttgggataa catgacctgg atacaatggg aaagggaagt cagcaattac 1860 acacaacaaa tatacagcct aattgaagaa tcgcagaacc agcaggaaaa gaatgaacaa 1920 gacttattgg cattggacaa gtgggcaagt ttgtggaact ggtttgacat aacaaaatgg 1980 ctatggtata taaaaatatt tataatgata gtaggaggtt taataggttt aagaatagtt 2040 tttgctgtgc tttctatagt aaatagagtt aggcagggat actcaccttt gtcattccag 2100 acccttaccc accaccagag ggaacccgac aggcccgaaa gaatcgaaga aggaggtgga 2160 gagcaagaca gagacagatc agtgcgctta gtgagcggat tcttagcact tgcctgggac 2220 gacctgcgga acctgtgcct cttcagctac caccgattga gagacttagt cttgattgca 2280 gcgaggacag cagaactcct gagacgcagc agtctccagg gactgagact ggggtgggag 2340 ggcctcaaat atctgtggaa tctcctgttg tattggggtc gggaactaaa gaatagtgct 2400 attaatttga ttgatacaat agcaatagca gtagctaact ggacagatag ggttatagaa 2460 gtagcacaag gagcttgtag agctattctc aacataccta gaaggataag acaaggcttg 2520 gaaagagctt tgctataa 2538 55 621 DNA Human immunodeficiency virus type 1 isolate=92NG003; gene=nef 55 ataggaggca agtggtcaaa aagtagcata gttggatggc ccgcggtaag ggagagaata 60 agacaaaccc ctccagcaga aggagtagga gcagcacctc aagacttagc taggcatgga 120 gcaatcacaa gcagcaatac agcacaaact aatcctgatt gtgcctggct agaagcacaa 180 caggagaatt cagaggtagg ctttccagtc agacaacagg tacctttgag accaatgact 240 tataaggctg cctttgatct cagcttcttt ttaaaagaaa aggggggact ggatgggcta 300 atttactcta agaaaagaca agacatcctt gacctatggg tctataatac acaaggatac 360 ttcccagatt ggcagaacta cactccaggg ccagggacta gattcccact gacatttcgg 420 tggtgcttca aactagtacc aatggatcca gcagagatag aggaagccaa taaaggagag 480 aacaacagtt tattacaccc tatctgccaa catggcctgg aagatgcgga cagagaagtg 540 ctggtatgga gatttgacag tagcctagca cggagacaca tagcccgaga acaacatccg 600 gagtactata aggactgctg a 621 56 1438 DNA Human immunodeficiency virus type 1 isolate=93BR029; gene=gag 56 atgggtgcga gagcgtcagt aataagcggg ggagaattag ataaatggga aaaaattagg 60 ttaaggccag gaggacataa aaaatataga ttaaaacata tagtatgggc aagcagggga 120 gctagaacga ttcgcagtta atcctggcct tttagagaca tcagaaggct gtagacaaat 180 actggaacag ctacaaccag cccttaagac gggatcagaa gaacttagat cattatataa 240 tacagtagca accctctatt gtgtacatca aaagatagat gtaaaagaca ccaaggaagc 300 tttagaaaag atagaggaag agcaaaacaa agtaagaaaa aggcacagca agcagcagct 360 aacacaggaa acaacagcca ggtcagccaa aattacccta tagtgcagaa ccttcagggg 420 caaatggtac accaggccat atcacctaga actttaaatg catgggtaaa agtagtagaa 480 gagaaggctt ttagcccaga agtaataccc atgttttcag cattatcaga aggagccacc 540 ccacaagatt taaacaccat gctaaacaca gtggggggac atcaagcagc tatgcaaatg 600 ttaaaagaaa ccatcaatga ggaagctgca gaatgggaca gagtacatcc agtgcatgca 660 ggacctatcc caccaggcca gatgagggaa cctaggggaa gtgatatagc tggaactact 720 agtacccttc aggaacaaat acaatggatg acaagcaacc cacctgtccc agtgggagaa 780 atttataaaa gatggatcat cctaggatta aataaaatag taagaatgta tagccctacc 840 agcattctgg gcataagaca aggaccaaag gaacccttta gagactatgt agatcgattt 900 tataaaactc taagagcaga gcaaacttca caggatgtaa aaaattggat gacagaaacc 960 ttgttggtcc aaaatgcgaa cccagattgc aaaaccattt taaaagcatt gggaccagca 1020 gctacactag aagaaatgat gacagcatgt cagggagtgg ggggacccgg ccataaagca 1080 agagttttgg cagaagcaat gagccaagta acaaattcag gtaccataat gatgcagaga 1140 ggcaatttta ggaaccaaag aaagactatt aagtgtttca attgtggcaa agaagggcac 1200 atagccaaaa attgcagggc ccctaggaaa aagggctgct ggaaatgtgg aaaggaagga 1260 caccagatga aagattgtac tgagagacag gctaattttt tagggaaaat ctggccttcc 1320 cacaagggaa ggccagggaa tttccttcag agcagaccag agccaacagc cccaccagca 1380 gagagcttca ggtttgggga agaggtaaca actccctctc agaaacagga gccgatag 1438 57 3012 DNA Human immunodeficiency virus type 1 isolate=93BR029; gene=pol; note=NH2-terminus uncertain 57 ttttttaggg aaaatctggc cttcccacaa gggaaggcca gggaatttcc ttcagagcag 60 accagagcca acagccccac cagcagagag cttcaggttt ggggaagagg taacaactcc 120 ctctcagaaa caggagccga tagacaagga gatgtatcct ttggcttccc tcagatcact 180 ctttggcaac gacccctcgt cacagtaaag ataggggggc aactaaagga agccctatta 240 gataccggag cagatgatac agtattagaa gaaataaatt taccaggaag atggaaacca 300 aaaatgatag ggggaattgg aggttttatc aaagtaagac agtatgatca aatacccata 360 gaaatttgtg gacgtaaagc tacaggtaca gtattagtag gacctacacc tgtcaacata 420 attggaagaa atctgttgac tcagattggc tgcactttaa attttcccat tagtcctatt 480 gaaactgtac cagtaaaatt gaagccagga atggatggcc caagggttaa acaatggcca 540 ttgacagaag aaaaaataaa agcattaaca gaaatatgta cagaaatgga aaaagaagga 600 aaaatttcaa aaattgggcc cgaaaatcca tacaatactc cagtatttgc cataaagaaa 660 aaagatagta ctaaatggag aaaattagta gatttcagag aacttaataa gagaactcaa 720 gacttctggg aagttcagtt agggatacca catcccgcag ggttaaagaa gaaaaaatca 780 gtaacagtac tggatgtggg tgatgcatat ttttcagttc cattagataa agacttcagg 840 aagtatactg catttaccat acctagtaca aacaatgaaa caccagggct tagatatcag 900 tacaatgtgc ttccacaggg gtggaaagga tcaccagcaa tattccaaag tagcatgaca 960 aaaatcttag agccttttag aaaacaaaat ccagacatag ttatctatca atacatggat 1020 gatttgtatg taggatctga cttagaaata gggcagcata gaactaagat agaggaattg 1080 agacagcatt tgttgaggtg gggatttacc acaccagaca aaaaacatca gaaagaacct 1140 ccattccttt ggatgggtta tgaactccat cctgataaat ggacagtaca gcctatagtg 1200 ctgccagaaa aagacagctg gactgtcaat gacatacaga agttagtggg aaaattgaat 1260 tgggcaagtc agatttatgc agggattaaa gtaaggcaat tatgtaaact ccttagggga 1320 accaaagcac taacagaagt agtaccacta acagcagagg cagagctaga actggcagaa 1380 aacagggaga ttctaaaaga accagtacat ggagtgtatt atgacccctc aaaagactta 1440 atagcagaaa tacagaaaca ggggcaaggc caatggacat atcaaattta tcaagagcca 1500 tataaaaatt tgaaaacagg aaagtatgca aggatgaggg gtgcccacac taatgatgta 1560 aaacaactaa cagaggcagt gcaaaaaata accacagaaa gcatagtaat atggggaaag 1620 attcctaaat ttaaactacc catacaaaaa gaaacgtggg aagcatggtg gatagagtat 1680 tggcaagcca cctggattcc tgagtgggag tttgtcaata cccctccctt agtgaaatta 1740 tggtaccagt tagagaaaga acccatagta ggagcagaaa ctttctatgt agatggggca 1800 gctaataggg aaactaaatt aggaaaagca ggatatgtga ctgacagagg aagacaaaaa 1860 gttgtccccc taacggacac aacaaatcag aaaactgagt tacaagcaat tcatctagct 1920 ttgcaggatt cgggattaga agtaaacata gtaacagact cacaatatgc attaggaatc 1980 attcaagcac aaccagataa gagtgaatta gaaatagtca atcaaataat agagcagtta 2040 ataaaaaagg aaaagatcta cctggcatgg gtaccagcac acaaaggaat tggaggaaat 2100 gaacaagtag acaaattagt cagttctgga atcaggaaag tactattttt agatggaata 2160 gataaggccc aagaagaaca tgagaaatat cacaataatt ggagagcaat ggctagtgac 2220 tttaacatac cacctgtagt agcaaaagaa atagtagcca gctgtgataa atgtcagcta 2280 aaaggagaag ccatgcatgg acaagtagac tgtagtccag gaatatggca gctagattgt 2340 acacacttag aaggaaaagt tatcctggta gcagtgcatg tagccggtgg atatatagaa 2400 gcagaagtta ttccagcaga gacagggcaa gaaacagcat actttctctt aaaattagca 2460 ggaagatggc cagtaaaaac aatacacaca gacaatggca gcaatttcac cagtactaca 2520 gtcaaggccg cctgttggtg ggcggggatc aagcaggaat ttggcattcc ctacaatccc 2580 caaagtcaag gagtaataga atctatgaat aaagaattaa agaaaattat aggacaggta 2640 agggatcagg ctgaacatct taagacagca gtacaaacgg cagtattcat ccacaatttt 2700 aaaagaaaag gggggattgg ggggtacagt gcaggggaaa gaatagtaga cataatagca 2760 acagacatac agactaaaga attacaaaaa caaattacaa aaattcaaaa ttttcgggtt 2820 tattacagag acagcagaga tccactttgg aaaggaccag caaagcttct ctggaaaggt 2880 gaaggggcag tagtaataca agataatagt gacataaaag tagtgccaag aagaaaagta 2940 aagatcatta gggattatgg aaaacagatg gcaggtggtg attgtgtggc aggtagacag 3000 gatgaggatt aa 3012 58 579 DNA Human immunodeficiency virus type 1 isolate=93BR029; gene=vif 58 atggaaaaca gatggcaggt ggtgattgtg tggcaggtag acaggatgag gattaacaca 60 tggaaaagtt tagtaaaata ccatatgcat gtttcaaaga aagccaaaag atggttttat 120 agacatcact ttgaaagcag gcatccaaga gtaagttcag aagtacatat cccactagag 180 gaagctaaat tagtaataac aacatattgg gggctgcata caggagaaag agattggcat 240 ctgggtcagg gagtctccat agaatggagg caggggaggt ataggacaca aatagaccct 300 ggcctggcag accaactgat ccatatatat tattttgatt gtttttcaga atctgccata 360 aggaaagcca tattaggaca tagaattagc cctaggtgtg attatcaagc aggacataac 420 aaggtaggat ctctacagta cttggcacta acagcattaa taaaaccaaa aaagagaaag 480 ccacctttgc ccagtgttaa gaaactgaca gaggatagat ggaacaagcc ccagaagacc 540 aaggaccaca gagggagcca tacaatgaat ggacactag 579 59 291 DNA Human immunodeficiency virus type 1 isolate=93BR029; gene=vpr 59 atggaacaag ccccagaaga ccaaggacca cagagggagc catacaatga atggacacta 60 gaacttttag aggaacttaa gagtgaagct gttagacatt ttcctaggtt atggctccat 120 agcttaggac aacatatcta tgaaacttat ggggatactt gggcaggagt ggaagccata 180 ataagaattc tgcaacaact gctgtttatt catttcagaa ttggatgtca acatagcaga 240 ataggcatta atcgacagag gagagcaagg aatggagcca gtagatccta g 291 60 2601 DNA Human immunodeficiency virus type 1 isolate=93BR029; gene=tat 60 atggagccag tagatcctag actagagccc tggaagcatc caggaagtcg gcctcagacg 60 gcttgtaata gttgctattg taaaaagtgt tgctttcatt gtcaagtttg tttcacaaca 120 aagggcttag gcatctccta tggcaggaag aagcggagac agcgacacag aactcctcaa 180 agcagtcagc tacatcaaga tcctgtacca aagcagtaag tattgttaag taatatatgt 240 aatgtcatat ttgttagtaa taggtttagc agcattaata gcagcactaa taatagcaat 300 agttgtgtgg actatagcat atatagaata tagggaacta gtaaggcaaa gaaaaataaa 360 taggttatat aaaagaataa gagaaagagc agaagacagt ggcaatgaga gtgaggggga 420 tgcagaggaa ttggcagcac ttggggaaat ggggcctttt attcctgggg atattgataa 480 tctgtaatgc tgaaaacttg tgggtcacag tctattatgg ggtacctgtg tggaaagaag 540 caaccactac tttattctgt gcatcagatg ctaaagcata tgaaaaagaa gcacataatg 600 tctgggctac acatgcctgt gtacccacag atcccaatcc acaagaagta gttctggaaa 660 atgtaacaga aaattttgat atgtggaaaa ataacatggt agaacaaatg catacagata 720 taatcagttt atgggatcaa agcctgaagc catgtgtgaa gttaacccca ctctgtgtta 780 ctttacgttg tagtaatgcc actaccaaca gtactcaaaa cgacaccctg aaggaagagc 840 caggggcaat acaaaactgt tctttcaata tgaccacaga agtaagagat aagcagctga 900 aagtacatgc acttttttat aggcttgata tagtaccaat cagcaatgat aatagtagca 960 atgataatag tagcagagaa tacaggctaa taaattgtaa tacctcaacc cttacacagg 1020 cttgtccaaa ggtatcttgg gatccaattc ccatacatta ttgtgctcca gctgggtatg 1080 cgattctaaa gtgtaatgat aaaaaattca atgggacggg gccatgcagg aatgtcagca 1140 cagtacaatg tacacatgga attaaaccag tggtatcaac tcaattgttg ttaaatggca 1200 gcctagcaga aaaagatata ataatcagat ctcaaaatat ctcagataat gcaaaaacca 1260 taatagtaca acttaatgta tctgtgccga ttaattgtac aagacccaac aacaatacaa 1320 gaaaaagtat accaatagga ccaggacgag cattttatac aacaggagaa ataataggag 1380 acatcagaaa ggcacattgt aacgttagtg gaacaaaatg gaatgagacg ttagaaaagg 1440 taagggcaaa gttaaagcct catttcccta atgcaacaat aaaatttaac tcatcctcag 1500 gaggggacct agaaattaca atgcatagtt ttaattgtag aggagaattt ttctactgca 1560 atacatcagg actgtttaat gacacagtag acaatggcac tatcactctc ccatgtcgaa 1620 taaagcaaat tgtaaatatg tggcaggaag tggggcgagc aatgtatgcc gctcccattg 1680 caggaaacat tacctgtagc tcaaatatta caggtctact attgacaaga gatggtggtc 1740 agaataatca gacggaggag accttcagac ctgggggagg aaatatgaaa gacaactgga 1800 gaagtgaatt atataaatat aaagtagtag aaattgagcc attaggagta gcacccacca 1860 aggcaaaaag acaagtggtg aagagagaaa aaagagcagt gggaatggga gctttgttcc 1920 ttgggttctt gggagcagca ggaagcacta tgggcgcagc gtcaataacg ctgacggcac 1980 aggccagaca attattgtct ggcatagtgc aacagcagaa taatttgctg agggctattg 2040 aagcgcaaca gcatctgttg cagctcacag tctggggcat taaacagctc caggcaagaa 2100 tcctggctgt ggaaagatac ctaaaggatc aacagctcct agggctttgg ggctgctctg 2160 gaaaactcat ctgcaccact gatgtgccct ggaactctag ttggagtaac aaatctcagg 2220 agaagatctg ggggaacatg acctggatgg agtgggaaaa agagattagc aattactcaa 2280 acgaaatata taggttaatt gaagagtcgc agaaccagca ggaaaagaat gaacaagaat 2340 tattggcatt ggacaaatgg gcaagtctgt ggaattggtt tgacatatca aaatggctgt 2400 ggtatataaa aatattcata atgatagtag gaggcttgat aggcttaaga atagtttttg 2460 ctgtgctttc tatagtaaat agagttagga agggatactc acctttgtca ttacagaccc 2520 gcttcccaag cccaagggaa cccgacaggc ccgaaggaat cgaagaagga ggtggagagc 2580 caggcaaaga cagatccgtg a 2601 61 2652 DNA Human immunodeficiency virus type 1 isolate=93BR029; gene=rev 61 atggcaggaa gaagcggaga cagcgacaca gaactcctca aagcagtcag ctacatcaag 60 atcctgtacc aaagcagtaa gtattgttaa gtaatatatg taatgtcata tttgttagta 120 ataggtttag cagcattaat agcagcacta ataatagcaa tagttgtgtg gactatagca 180 tatatagaat atagggaact agtaaggcaa agaaaaataa ataggttata taaaagaata 240 agagaaagag cagaagacag tggcaatgag agtgaggggg atgcagagga attggcagca 300 cttggggaaa tggggccttt tattcctggg gatattgata atctgtaatg ctgaaaactt 360 gtgggtcaca gtctattatg gggtacctgt gtggaaagaa gcaaccacta ctttattctg 420 tgcatcagat gctaaagcat atgaaaaaga agcacataat gtctgggcta cacatgcctg 480 tgtacccaca gatcccaatc cacaagaagt agttctggaa aatgtaacag aaaattttga 540 tatgtggaaa aataacatgg tagaacaaat gcatacagat ataatcagtt tatgggatca 600 aagcctgaag ccatgtgtga agttaacccc actctgtgtt actttacgtt gtagtaatgc 660 cactaccaac agtactcaaa acgacaccct gaaggaagag ccaggggcaa tacaaaactg 720 ttctttcaat atgaccacag aagtaagaga taagcagctg aaagtacatg cactttttta 780 taggcttgat atagtaccaa tcagcaatga taatagtagc aatgataata gtagcagaga 840 atacaggcta ataaattgta atacctcaac ccttacacag gcttgtccaa aggtatcttg 900 ggatccaatt cccatacatt attgtgctcc agctgggtat gcgattctaa agtgtaatga 960 taaaaaattc aatgggacgg ggccatgcag gaatgtcagc acagtacaat gtacacatgg 1020 aattaaacca gtggtatcaa ctcaattgtt gttaaatggc agcctagcag aaaaagatat 1080 aataatcaga tctcaaaata tctcagataa tgcaaaaacc ataatagtac aacttaatgt 1140 atctgtgccg attaattgta caagacccaa caacaataca agaaaaagta taccaatagg 1200 accaggacga gcattttata caacaggaga aataatagga gacatcagaa aggcacattg 1260 taacgttagt ggaacaaaat ggaatgagac gttagaaaag gtaagggcaa agttaaagcc 1320 tcatttccct aatgcaacaa taaaatttaa ctcatcctca ggaggggacc tagaaattac 1380 aatgcatagt tttaattgta gaggagaatt tttctactgc aatacatcag gactgtttaa 1440 tgacacagta gacaatggca ctatcactct cccatgtcga ataaagcaaa ttgtaaatat 1500 gtggcaggaa gtggggcgag caatgtatgc cgctcccatt gcaggaaaca ttacctgtag 1560 ctcaaatatt acaggtctac tattgacaag agatggtggt cagaataatc agacggagga 1620 gaccttcaga cctgggggag gaaatatgaa agacaactgg agaagtgaat tatataaata 1680 taaagtagta gaaattgagc cattaggagt agcacccacc aaggcaaaaa gacaagtggt 1740 gaagagagaa aaaagagcag tgggaatggg agctttgttc cttgggttct tgggagcagc 1800 aggaagcact atgggcgcag cgtcaataac gctgacggca caggccagac aattattgtc 1860 tggcatagtg caacagcaga ataatttgct gagggctatt gaagcgcaac agcatctgtt 1920 gcagctcaca gtctggggca ttaaacagct ccaggcaaga atcctggctg tggaaagata 1980 cctaaaggat caacagctcc tagggctttg gggctgctct ggaaaactca tctgcaccac 2040 tgatgtgccc tggaactcta gttggagtaa caaatctcag gagaagatct gggggaacat 2100 gacctggatg gagtgggaaa aagagattag caattactca aacgaaatat ataggttaat 2160 tgaagagtcg cagaaccagc aggaaaagaa tgaacaagaa ttattggcat tggacaaatg 2220 ggcaagtctg tggaattggt ttgacatatc aaaatggctg tggtatataa aaatattcat 2280 aatgatagta ggaggcttga taggcttaag aatagttttt gctgtgcttt ctatagtaaa 2340 tagagttagg aagggatact cacctttgtc attacagacc cgcttcccaa gcccaaggga 2400 acccgacagg cccgaaggaa tcgaagaagg aggtggagag ccaggcaaag acagatccgt 2460 gagattagtg aacggattct tagctcttgt ctgggacgac ctgaggaacc tgtgcctctt 2520 cagctaccgc cacttgagag acttcatatt aattgcagcg aggattgtgg acaggggact 2580 gaagaggggg tgggaagccc tcaaacttct ggggaatctc gcgctgtatt ggagtcagga 2640 actaaagaat ag 2652 62 2529 DNA Human immunodeficiency virus type 1 isolate=93BR029; gene=env 62 atgagagtga gggggatgca gaggaattgg cagcacttgg ggaaatgggg ccttttattc 60 ctggggatat tgataatctg taatgctgaa aacttgtggg tcacagtcta ttatggggta 120 cctgtgtgga aagaagcaac cactacttta ttctgtgcat cagatgctaa agcatatgaa 180 aaagaagcac ataatgtctg ggctacacat gcctgtgtac ccacagatcc caatccacaa 240 gaagtagttc tggaaaatgt aacagaaaat tttgatatgt ggaaaaataa catggtagaa 300 caaatgcata cagatataat cagtttatgg gatcaaagcc tgaagccatg tgtgaagtta 360 accccactct gtgttacttt acgttgtagt aatgccacta ccaacagtac tcaaaacgac 420 accctgaagg aagagccagg ggcaatacaa aactgttctt tcaatatgac cacagaagta 480 agagataagc agctgaaagt acatgcactt ttttataggc ttgatatagt accaatcagc 540 aatgataata gtagcaatga taatagtagc agagaataca ggctaataaa ttgtaatacc 600 tcaaccctta cacaggcttg tccaaaggta tcttgggatc caattcccat acattattgt 660 gctccagctg ggtatgcgat tctaaagtgt aatgataaaa aattcaatgg gacggggcca 720 tgcaggaatg tcagcacagt acaatgtaca catggaatta aaccagtggt atcaactcaa 780 ttgttgttaa atggcagcct agcagaaaaa gatataataa tcagatctca aaatatctca 840 gataatgcaa aaaccataat agtacaactt aatgtatctg tgccgattaa ttgtacaaga 900 cccaacaaca atacaagaaa aagtatacca ataggaccag gacgagcatt ttatacaaca 960 ggagaaataa taggagacat cagaaaggca cattgtaacg ttagtggaac aaaatggaat 1020 gagacgttag aaaaggtaag ggcaaagtta aagcctcatt tccctaatgc aacaataaaa 1080 tttaactcat cctcaggagg ggacctagaa attacaatgc atagttttaa ttgtagagga 1140 gaatttttct actgcaatac atcaggactg tttaatgaca cagtagacaa tggcactatc 1200 actctcccat gtcgaataaa gcaaattgta aatatgtggc aggaagtggg gcgagcaatg 1260 tatgccgctc ccattgcagg aaacattacc tgtagctcaa atattacagg tctactattg 1320 acaagagatg gtggtcagaa taatcagacg gaggagacct tcagacctgg gggaggaaat 1380 atgaaagaca actggagaag tgaattatat aaatataaag tagtagaaat tgagccatta 1440 ggagtagcac ccaccaaggc aaaaagacaa gtggtgaaga gagaaaaaag agcagtggga 1500 atgggagctt tgttccttgg gttcttggga gcagcaggaa gcactatggg cgcagcgtca 1560 ataacgctga cggcacaggc cagacaatta ttgtctggca tagtgcaaca gcagaataat 1620 ttgctgaggg ctattgaagc gcaacagcat ctgttgcagc tcacagtctg gggcattaaa 1680 cagctccagg caagaatcct ggctgtggaa agatacctaa aggatcaaca gctcctaggg 1740 ctttggggct gctctggaaa actcatctgc accactgatg tgccctggaa ctctagttgg 1800 agtaacaaat ctcaggagaa gatctggggg aacatgacct ggatggagtg ggaaaaagag 1860 attagcaatt actcaaacga aatatatagg ttaattgaag agtcgcagaa ccagcaggaa 1920 aagaatgaac aagaattatt ggcattggac aaatgggcaa gtctgtggaa ttggtttgac 1980 atatcaaaat ggctgtggta tataaaaata ttcataatga tagtaggagg cttgataggc 2040 ttaagaatag tttttgctgt gctttctata gtaaatagag ttaggaaggg atactcacct 2100 ttgtcattac agacccgctt cccaagccca agggaacccg acaggcccga aggaatcgaa 2160 gaaggaggtg gagagccagg caaagacaga tccgtgagat tagtgaacgg attcttagct 2220 cttgtctggg acgacctgag gaacctgtgc ctcttcagct accgccactt gagagacttc 2280 atattaattg cagcgaggat tgtggacagg ggactgaaga gggggtggga agccctcaaa 2340 cttctgggga atctcgcgct gtattggagt caggaactaa agaatagtgc tattagcttg 2400 cttaatacca cagcaatagt agtagctgag gggacagata gagttataga agctttgcaa 2460 agagcgggta gagctgttct taacgtacct agaagaataa gacagggctt ggaaagggct 2520 ttgctataa 2529 63 621 DNA Human immunodeficiency virus type 1 isolate=93BR029; gene=nef 63 atgggtagca agtggtcaaa aagtagtata gttgggtggc ctgctataag ggaaagatta 60 agacaaaccc ctccagcagc agaaggggtg ggagcagtgt ctcaagactt agaaagacgg 120 ggggcaatta caagcagcaa tactggagct aataatcctg acttggcctg gctggaggca 180 caagaggaag aggaagtagg ctttccagtc agacctcagg tacctttaag accaatgact 240 tataagggag ctcttgatct cagtcacttt ttaaaagaaa aggggggact ggaagggtta 300 atttattcca agaaaagaca agagatcctt gatctgtggg tttaccacac acaaggctac 360 ttccctgatt ggcagaacta cacaccaggg ccagggacca gatatccact gaccttaggg 420 tggtgcttca agctagtacc agttgaccca gaggaggtag aaaaggccaa tgaaggagag 480 aacaactgct tgctacaccc catgagccaa catggaatgg aggatgaaga cagagaaata 540 ctgcagtgga ggtttgacag ccgcctagca tttcatcaca tggcccgaga gctgcatccg 600 gagtactaca aggactgctg a 621 64 1503 DNA Human immunodeficiency virus type 1 isolate=94CY032.3; gene=gag 64 atgggtgcga gagcgtcagt attaagtggg ggaaaattag atgcatggga gaggattcgg 60 ttaaggccag ggggaaagaa aaaatataga ctgaaacatc tagtatgggc aagcagagag 120 ttggaaagat tcgcacttaa ccctggcctt ttagaaacag cagaaggatg tcaacaatta 180 atggaacagt tacaatcaac tctcaaaaca ggatcagaag aacttagatc attatataat 240 actataacaa ccctctggtg cgtacatcaa agaatagatg tacaagacac caaggaagct 300 ttagataaaa tagaggaaat acaaagtaag agcaagcaaa agacacagca ggcagcagct 360 gccgcaggag gtagcagcaa tgtcagccaa aattacccta tagtgcaaaa tgcacaaggg 420 caaatggtac atcagagcat ttcacctaga actttgaatg catgggtaaa agtaatagaa 480 gaaaaggctt tcagcccaga agtaataccc atgttctcag cattatcaga gggagccacc 540 ccacaagatt tgaacatgat gctaaatata gtggggggac accaggcagc aatgcaaatg 600 ttaaaagata ccatcaatga ggaagctgca gactgggaca ggacacatcc agtacatgca 660 gggcctattc caccaggcca gatgagagaa ccaaggggaa gtgatatagc aggaactact 720 agtacccttc aagaacaaat aggatggatg acaagcaacc cacctgtccc agtgggagaa 780 atctataaaa gatggataat cttggggtta aataaaatag taagaacgta tagccccatt 840 agcatcttgg acataagaca aggaccaaaa gaacccttca gagattatgt agataggttc 900 tttaaatgtc tcagagcaga acaagctacc caggaggtga aaaattggat gacagaaacc 960 ctgctggtcc aaaatgcgaa tccagactgt aagtccatct taaaagcatt aggaacaggg 1020 gctacattag aagaaatgat gacagcatgt cagggagtgg gaggacccag ccataaagca 1080 agagttttag ctgaggcaat gagccaggca tcaaatgcag cagcagccat aatgatgcag 1140 aaaagcaaat ttaagggcca aagaagaact attaagtgtt tcaactgtgg caaggaagga 1200 catctagcca gaaattgcag ggcccctagg aaaaagggct gctggaagtg tggaaaggag 1260 ggacatcaaa tgaaagactg cactgagaga caggctaatt ttttagggag aatgtggcct 1320 tccagcaaag ggaggccagg aaattttctt cagaacaggc cagagccaac agccccgccc 1380 gcggaatgct tagagaggaa agaggagaca acctcctctc tgaagcagga accgagggac 1440 aaggaactat atcctttaac ttccctcaaa tcactctttg gcagcgaccc cttgtcacaa 1500 taa 1503 65 3009 DNA Human immunodeficiency virus type 1 isolate=94CT032.3; gene=pol 65 ttttttaggg agaatgtggc cttccagcaa agggaggcca ggaaattttc ttcagaacag 60 gccagagcca acagccccgc ccgcggaatg cttagagagg aaagaggaga caacctcctc 120 tctgaagcag gaaccgaggg acaaggaact atatccttta acttccctca aatcactctt 180 tggcagcgac cccttgtcac aataaaacta gggggacaga taagggaggc tcttttagat 240 acaggagcag atgatacagt attagaagaa ataaatttgc caggaaaatg gaagccaaaa 300 atgatagggg gaatcggagg ttttatcaaa gtaagacaat atgatcagat acctatagaa 360 atttgtggaa aaaaggccat aggcacagtg ttagtaggac ctacacctgt caacataatt 420 ggacgaaaca tgttgactca gcttggttgt actttaaatt ttccaattag tcctattgaa 480 actgtaccag taaaattaaa gccaggaatg gatggcccaa aggttaaaca atggccattg 540 acagaagaaa aaataaaagc cttaacagag atatgtacag acatggaaaa ggaaggcaag 600 atttcaaaaa ttgggcctga aaatccatac aatactccaa tatttgctat aaagaaaaaa 660 gacagcacta aatggagaaa attagtagat ttcagagaac tcaataaaag aactcaggac 720 ttctgggaag ttcagttagg aataccgcac ccagcagggt taaagaagaa aaaatcagta 780 acagtattgg atgtggggga tgcatatttt tcagttccct tagatccaga gttcaggaag 840 tacactgcat tcaccatacc tagtaccaac aatgagacac caggaattag atatcagtac 900 aatgtgcttc cacagggctg gaaaggatca ccagcaatat tccaatgtag catgacaaaa 960 atcttagagc cctttagatt caaaaaccca gaaatagtca tataccaata tatggatgat 1020 ttgtatgtag ggtctgactt agaaataggg caacatagag caaaaataga agagctaaga 1080 gagcatctat tgagatgggg attcaccaca ccagacaaaa aacatcagaa agaaccccca 1140 tttctttgga tggggtatga actccatcct gacaaatgga cagtgcagcc tatacaaccg 1200 gcagaaaagg atagctggac tgtcaacgat atccagaagt tagtgggaaa actaaattgg 1260 gcaagtcaga tttatccagg gattaaagta aagcaattat gtaaacttct taggggagct 1320 aaagccctaa cagacatagt accactaact acagaggcag agttagaatt agcagagaac 1380 agggagattc taaaagaacc agtacatggg gcatattatg acccatcaaa agacttaata 1440 gcagaaatac agaagcaagg gcaaggtcaa tggacatatc aaatatatca agagccacat 1500 aaaaatctga aaacagggaa gtatgcaaga accagatctg cccacactaa tgatgttaga 1560 caattaacag aagcagtgca aaagatagcc atggaatgca tagtaatatg gggaaagact 1620 cctaagttta gattacccat acaaaaggaa acatgggaca catggtggac agaatattgg 1680 caggccacct ggatccctga atgggaattt gtcaataccc ctcctctagt aaaattatgg 1740 taccagttag aaacagaccc catagcagga gcagaaactt tctatgtaga tggggcagct 1800 aatagagaaa caaaacaggg aaaagcagga tatgttactg atagaggcag acaaaaagtt 1860 gtctccctat ctgaaacaac aaatcagaag actgaattac aagcaattta cttagctttg 1920 caggattcag gatcagaagt aaacatagta acagactcac agtatgcaat aggaatcatt 1980 caagcacaac cagatagaag tgaatcagat ttagttaatc aaataataga gcagttaata 2040 cggaaggaca aggtctacct gtcatgggta ccagcacaca aagggattgg aggaaatgaa 2100 caagtagata aattagtcag caatggaatc agaaaggtgc tatttttaga tggaatagat 2160 aaggctcaag aagaacatga gaaatatcac aataactgga gagcaatggc tagtgatttt 2220 aatctgccat cagtggtagc aaaagagata gtagctagct gtaataaatg tcagctaaaa 2280 ggggaagcca tgcatggaca agtggactgt agtccaggga tatggcagtt agattgtaca 2340 catttagaag gtaaagttat catggtagca gttcatgtgg ctagtggata catagaagca 2400 gaagttatcc cagcagaaac aggacaggaa acagcctact tcatactaaa attagcagga 2460 agatggccag tgaaaatgat acatgcagac aacggcccca atttcaccag tgctgcggtt 2520 aaggcagcct gttggtgggc agatatcaac caggaatttg gaattcccta caatccccaa 2580 agccaaggag tagtggaatc tatgaataaa gaattaaaga aaatcatagg gcaggtcagg 2640 gatcaagctg aacaccttaa gacagcagta cagatggcag tattcattca caattttaaa 2700 agaaaagggg ggattggggg gtacagtgca ggggaaagaa taatagacat aatagcatca 2760 gatatacaaa ctaaagaact acaaaaacaa attacaaaaa ttcaaaattt tcgggtttat 2820 tacagggaca gcagagaacc aatttggaag ggaccagcaa aactactctg gaaaggtgaa 2880 ggggcagtag taatacagga caacagtgat atcaaagtag taccaagaag aaaagcaaag 2940 attattaggg actatggcaa acagatggca ggtaatgatt gtgtggcagg tagacaggat 3000 gaagattag 3009 66 579 DNA Human immunodeficiency virus type 1 isolate=94CT032.3; gene=vif 66 atggcaaaca gatggcaggt aatgattgtg tggcaggtag acaggatgaa gattagaaca 60 tggaacagtc tagtgaaaca tcatatgtat gtttcaaaga aagctaaagg atgattctat 120 agacatcact atgaaagtag gcacccaaaa gtaagttcag aagtacatat cccactaggg 180 gaggctagat tagtagtaag aacatattgg ggtctgcagc caggggaaca agactggcac 240 ttgggtcatg gagtctccat agaatggagg ctcagaagat atagcacaca agtggatcct 300 gacctggcag accaactaat tcatatgcat tactttgatt gtttttcaga atctgccata 360 aggaaagcca tattaggaca tagagttagt cctaggtgtg aatatcaagc aggacataat 420 aaggtaggat ccttacaata cctggcacta gcagcattaa tatccccaaa aaagacaaag 480 ccacctttgc ctagtgttaa gaaactagtg gaggatagat ggaacaagcc ccagaagacc 540 aggggccgca gagagaacca aataatgaat ggacactag 579 67 288 DNA Human immunodeficiency virus type 1 isolate=94CY032.3; gene=vpr 67 atggaacaag ccccagaaga ccaggggccg cagagagaac caaataatga atggacacta 60 gagcttttgg aggagcttaa aaatgaagct gttaggcatt ttcctagacc ctggctccat 120 ggcctaggac agcatatcta taacacttat ggagatacct gggaaggggt tgaagctata 180 ataagaattt tgcaacaact actgtttatt catttcagaa ttgggtgcca acatagtaga 240 ataggcatta ctcctcaaag gagaagaggc aggggatgga gccagtag 288 68 2643 DNA Human immunodeficiency virus type 1 isolate=94CT032.3; gene=tat 68 atggagccag tagatcctga cctagagccc tggaaccatc cgggaagtca gcctacaact 60 gattgtaaca agtgtttctg taaaaagtgt tgctggcatt gccaagtttg ctttctgaaa 120 aaaggcttag gcatctccta tggcaggaag aagcggaaac atcgacgagg atctcttcaa 180 ggcagcaagg gccatcaaaa tcttatacca aagcagtaag tattaagtat atgtaatgtt 240 attctgggaa atctgggcaa tagtaggact ggtagtagcg ctaattatag taatagtagt 300 gtggacttta gtatttatag aatataagaa attgagaagg caaaggagaa tagacagctt 360 gtacaataga ataagagaaa gagcagaaga cagtggcaat gagagtgatg gggatgcaga 420 ggaattatcc acacttgtgg gaatggggaa ctttgatcct tgggttggtg ataatctgta 480 gtgcctcaaa caacttgtgg gtcacagttt attatggggt acctgtgtgg agagacgcag 540 agaccaccct attttgtgca tcagaagcta aagcatatga gaaagaagta cataatatct 600 gggctacaca tgcctgtgta cccacagacc ccaacccaca agaagtagct ctgataaatg 660 taacagagaa ctttaacatg tggaaaaatg acatggtaga acagatgcat gaggatataa 720 tcagtttatg gaatgaaggc ctaaaaccat gtgcaaagct aacctctctc tgtgttactt 780 ttacatgtat taatgcaact actactaata gtaccaatgg cactgtgatt aaagaaggaa 840 taaaaaactg ctctttcgat ataaccacag aaataaggga taagaagaag aaagaatatg 900 cgcttttcta tagaattgat atagtgccaa ttaatgctag agtgccaatt aatggtagta 960 ataggaataa tagtacagaa gagtatatgt taataaattg taacgcctca accattaaac 1020 aggcttgccc aaaggtgtct tttgagccaa ttcccataca ttattgtgcc ccagctggtt 1080 ttgcaatttt aaagtgtaat gagaaaaatt tcactggatt agggccatgc acaaatgtca 1140 gctcggtacg atgcactcat ggaattaagc cagtggtatc aactcaattg ctgttaaatg 1200 gaagcttagc aacggaagag gtagtaatta gatctaaaaa tatcacagac aataccaaaa 1260 atataatagt acagcttgca aaggctgtaa aaattaattg taccagacct ggcaacaata 1320 caagaaaaag tgtacatata gggccaggac taacatggta tgcaacaggt gaaataatag 1380 gagatataag acaagcacat tgtaacatta gtggaaatga ttggaatgac accttaaaag 1440 tgataagtga agaattgaaa agactcttcc ctaataaaac aataaaattt gctccacccg 1500 taggagggga cctagaaatt acaacacata gctttaattg taaaggagaa tttttctatt 1560 gcaatacaac accactgttt aatagtacac acatgcaaaa tggtacaaac attacaagta 1620 cagattctac aaattcaacc atcacactcc aatgcagact aaaacaattt gtaaggatgt 1680 ggcaggaagt ggggcaagca atgtacgcct cccccattgc agggagcatt aactgcagct 1740 cagatattac aggaataata ttgacaagag atggtggtac taataatact gagatcttca 1800 gacctggagg aggagacatg agggacaatt ggagaagtga actatataaa tataaagtag 1860 taaagattga accaatagga gtagcaccca ataaggcaag gagacgagtg gtgcagagag 1920 aaaaatgagc agtgggaata ggggccatgt tccttgggtt cttgggagca gcaggaagca 1980 ctatgggcgc agcgtcaatg acgctgacgg tacaggccag acaattattg tccggcatag 2040 tgcagcagca gagcaatttg ctgagggcta tagaggctca acaacatctg ttgagactca 2100 cggtctgggg cattaaacag ctccaggcaa gagtcctggc tctggaaagc tacctaaagg 2160 atcaacagct cctaggaatt tggggctgct ctggaaaact catctgcacc actaatgtac 2220 cttggaactc tagttggagt aataaatctt ataatgatat atgggacaat atgacctggt 2280 tgcaatggga taaagaaatt aacaattaca cacaaataat atatgggtta cttgaagaat 2340 cacagaacca gcaggaaaag aatgagcaag acttattggc cttggacaag tgggcaagcc 2400 tgtggaattg gtttagcata acaaaatggc tatggtatat aaaaatattt ataatgatag 2460 taggaggctt gataggctta agaataattt ttgctgtgct ttctatagta aatagagtta 2520 ggcagggata ctcacctttg tctttgcaga cccttatccc aacaacccaa cggggactcg 2580 acaggcccgg aggaacagaa gaagaaggtg gcgagcaaga cagaagcaga tccattcgct 2640 tag 2643 69 2688 DNA Human immunodeficiency virus type 1 isolate=94CT032.3; gene=rev 69 atggcaggaa gaagcggaaa catcgacgag gatctcttca aggcagcaag ggccatcaaa 60 atcttatacc aaagcagtaa gtattaagta tatgtaatgt tattctggga aatctgggca 120 atagtaggac tggtagtagc gctaattata gtaatagtag tgtggacttt agtatttata 180 gaatataaga aattgagaag gcaaaggaga atagacagct tgtacaatag aataagagaa 240 agagcagaag acagtggcaa tgagagtgat ggggatgcag aggaattatc cacacttgtg 300 ggaatgggga actttgatcc ttgggttggt gataatctgt agtgcctcaa acaacttgtg 360 ggtcacagtt tattatgggg tacctgtgtg gagagacgca gagaccaccc tattttgtgc 420 atcagaagct aaagcatatg agaaagaagt acataatatc tgggctacac atgcctgtgt 480 acccacagac cccaacccac aagaagtagc tctgataaat gtaacagaga actttaacat 540 gtggaaaaat gacatggtag aacagatgca tgaggatata atcagtttat ggaatgaagg 600 cctaaaacca tgtgcaaagc taacctctct ctgtgttact tttacatgta ttaatgcaac 660 tactactaat agtaccaatg gcactgtgat taaagaagga ataaaaaact gctctttcga 720 tataaccaca gaaataaggg ataagaagaa gaaagaatat gcgcttttct atagaattga 780 tatagtgcca attaatgcta gagtgccaat taatggtagt aataggaata atagtacaga 840 agagtatatg ttaataaatt gtaacgcctc aaccattaaa caggcttgcc caaaggtgtc 900 ttttgagcca attcccatac attattgtgc cccagctggt tttgcaattt taaagtgtaa 960 tgagaaaaat ttcactggat tagggccatg cacaaatgtc agctcggtac gatgcactca 1020 tggaattaag ccagtggtat caactcaatt gctgttaaat ggaagcttag caacggaaga 1080 ggtagtaatt agatctaaaa atatcacaga caataccaaa aatataatag tacagcttgc 1140 aaaggctgta aaaattaatt gtaccagacc tggcaacaat acaagaaaaa gtgtacatat 1200 agggccagga ctaacatggt atgcaacagg tgaaataata ggagatataa gacaagcaca 1260 ttgtaacatt agtggaaatg attggaatga caccttaaaa gtgataagtg aagaattgaa 1320 aagactcttc cctaataaaa caataaaatt tgctccaccc gtaggagggg acctagaaat 1380 tacaacacat agctttaatt gtaaaggaga atttttctat tgcaatacaa caccactgtt 1440 taatagtaca cacatgcaaa atggtacaaa cattacaagt acagattcta caaattcaac 1500 catcacactc caatgcagac taaaacaatt tgtaaggatg tggcaggaag tggggcaagc 1560 aatgtacgcc tcccccattg cagggagcat taactgcagc tcagatatta caggaataat 1620 attgacaaga gatggtggta ctaataatac tgagatcttc agacctggag gaggagacat 1680 gagggacaat tggagaagtg aactatataa atataaagta gtaaagattg aaccaatagg 1740 agtagcaccc aataaggcaa ggagacgagt ggtgcagaga gaaaaatgag cagtgggaat 1800 aggggccatg ttccttgggt tcttgggagc agcaggaagc actatgggcg cagcgtcaat 1860 gacgctgacg gtacaggcca gacaattatt gtccggcata gtgcagcagc agagcaattt 1920 gctgagggct atagaggctc aacaacatct gttgagactc acggtctggg gcattaaaca 1980 gctccaggca agagtcctgg ctctggaaag ctacctaaag gatcaacagc tcctaggaat 2040 ttggggctgc tctggaaaac tcatctgcac cactaatgta ccttggaact ctagttggag 2100 taataaatct tataatgata tatgggacaa tatgacctgg ttgcaatggg ataaagaaat 2160 taacaattac acacaaataa tatatgggtt acttgaagaa tcacagaacc agcaggaaaa 2220 gaatgagcaa gacttattgg ccttggacaa gtgggcaagc ctgtggaatt ggtttagcat 2280 aacaaaatgg ctatggtata taaaaatatt tataatgata gtaggaggct tgataggctt 2340 aagaataatt tttgctgtgc tttctatagt aaatagagtt aggcagggat actcaccttt 2400 gtctttgcag acccttatcc caacaaccca acggggactc gacaggcccg gaggaacaga 2460 agaagaaggt ggcgagcaag acagaagcag atccattcgc ttagtgaacg gattcttgcc 2520 acttatctgg gacgacctgc ggaacctgtg cctcttcagc taccgccact tgagaaactt 2580 actcttaatt gtagcgagga ctgtggaact tctggggata agggggtggg aagccctcaa 2640 gtatctgtgg aacttcctgc tgtattgggg acaggagcta aagaatag 2688 70 246 DNA Human immunodeficiency virus type 1 isolate=94CT032.3; gene=vpu 70 atgttattct gggaaatctg ggcaatagta ggactggtag tagcgctaat tatagtaata 60 gtagtgtgga ctttagtatt tatagaatat aagaaattga gaaggcaaag gagaatagac 120 agcttgtaca atagaataag agaaagagca gaagacagtg gcaatgagag tgatggggat 180 gcagaggaat tatccacact tgtgggaatg gggaactttg atccttgggt tggtgataat 240 ctgtag 246 71 2571 DNA Human immunodeficiency virus type 1 isolate=94CY032.3; gene=env 71 atgagagtga tggggatgca gaggaattat ccacacttgt gggaatgggg aactttgatc 60 cttgggttgg tgataatctg tagtgcctca aacaacttgt gggtcacagt ttattatggg 120 gtacctgtgt ggagagacgc agagaccacc ctattttgtg catcagaagc taaagcatat 180 gagaaagaag tacataatat ctgggctaca catgcctgtg tacccacaga ccccaaccca 240 caagaagtag ctctgataaa tgtaacagag aactttaaca tgtggaaaaa tgacatggta 300 gaacagatgc atgaggatat aatcagttta tggaatgaag gcctaaaacc atgtgcaaag 360 ctaacctctc tctgtgttac ttttacatgt attaatgcaa ctactactaa tagtaccaat 420 ggcactgtga ttaaagaagg aataaaaaac tgctctttcg atataaccac agaaataagg 480 gataagaaga agaaagaata tgcgcttttc tatagaattg atatagtgcc aattaatgct 540 agagtgccaa ttaatggtag taataggaat aatagtacag aagagtatat gttaataaat 600 tgtaacgcct caaccattaa acaggcttgc ccaaaggtgt cttttgagcc aattcccata 660 cattattgtg ccccagctgg ttttgcaatt ttaaagtgta atgagaaaaa tttcactgga 720 ttagggccat gcacaaatgt cagctcggta cgatgcactc atggaattaa gccagtggta 780 tcaactcaat tgctgttaaa tggaagctta gcaacggaag aggtagtaat tagatctaaa 840 aatatcacag acaataccaa aaatataata gtacagcttg caaaggctgt aaaaattaat 900 tgtaccagac ctggcaacaa tacaagaaaa agtgtacata tagggccagg actaacatgg 960 tatgcaacag gtgaaataat aggagatata agacaagcac attgtaacat tagtggaaat 1020 gattggaatg acaccttaaa agtgataagt gaagaattga aaagactctt ccctaataaa 1080 acaataaaat ttgctccacc cgtaggaggg gacctagaaa ttacaacaca tagctttaat 1140 tgtaaaggag aatttttcta ttgcaataca acaccactgt ttaatagtac acacatgcaa 1200 aatggtacaa acattacaag tacagattct acaaattcaa ccatcacact ccaatgcaga 1260 ctaaaacaat ttgtaaggat gtggcaggaa gtggggcaag caatgtacgc ctcccccatt 1320 gcagggagca ttaactgcag ctcagatatt acaggaataa tattgacaag agatggtggt 1380 actaataata ctgagatctt cagacctgga ggaggagaca tgagggacaa ttggagaagt 1440 gaactatata aatataaagt agtaaagatt gaaccaatag gagtagcacc caataaggca 1500 aggagacgag tggtgcagag agaaaaatga gcagtgggaa taggggccat gttccttggg 1560 ttcttgggag cagcaggaag cactatgggc gcagcgtcaa tgacgctgac ggtacaggcc 1620 agacaattat tgtccggcat agtgcagcag cagagcaatt tgctgagggc tatagaggct 1680 caacaacatc tgttgagact cacggtctgg ggcattaaac agctccaggc aagagtcctg 1740 gctctggaaa gctacctaaa ggatcaacag ctcctaggaa tttggggctg ctctggaaaa 1800 ctcatctgca ccactaatgt accttggaac tctagttgga gtaataaatc ttataatgat 1860 atatgggaca atatgacctg gttgcaatgg gataaagaaa ttaacaatta cacacaaata 1920 atatatgggt tacttgaaga atcacagaac cagcaggaaa agaatgagca agacttattg 1980 gccttggaca agtgggcaag cctgtggaat tggtttagca taacaaaatg gctatggtat 2040 ataaaaatat ttataatgat agtaggaggc ttgataggct taagaataat ttttgctgtg 2100 ctttctatag taaatagagt taggcaggga tactcacctt tgtctttgca gacccttatc 2160 ccaacaaccc aacggggact cgacaggccc ggaggaacag aagaagaagg tggcgagcaa 2220 gacagaagca gatccattcg cttagtgaac ggattcttgc cacttatctg ggacgacctg 2280 cggaacctgt gcctcttcag ctaccgccac ttgagaaact tactcttaat tgtagcgagg 2340 actgtggaac ttctggggat aagggggtgg gaagccctca agtatctgtg gaacttcctg 2400 ctgtattggg gacaggagct aaagaatagt gctattaatt tgtttaatac cacagcaata 2460 gcagtagctg agggaacaga taggattata gaagcagtac agagagcttg tagagctatt 2520 tgcaacatac ctagaagaat cagacagggc cttgaaagag ctttgcttta a 2571 72 660 DNA Human immunodeficiency virus type 1 nef 72 atgggaggca aatggtcaaa aagtagcata gttggatggc ctgagataag ggaaagaatg 60 aggcgagctc gagctgagcc agaaagaatg aggcgagctc aagctgagcc agcagcagca 120 ggagtaggag cagtgtctca agacttggac aaacatgggg caatcacaat taacaataca 180 gcagctacta atcctgacaa aacctggctg gaagcacaag aagaggaaga agaggtaggt 240 tttccagtca ggccacaggt acctttaagg ccaatgacct ttaaaggagc tttagatctc 300 agccactttt taaaagaaaa ggggggactg gatgggctaa tttactccaa gaaaagacaa 360 gagatccttg atctgtgggt ctatcacaca caaggtttct tccctgattg ggataactac 420 acaccaggac caggggagag attcccactg tgctttggat ggtgcttcaa gctagtacca 480 gtagatccac aggaggtgga agaggccact gaaggagaga acacctgttt gctgcaccct 540 ataagccagc atggaatgga ggatgaagag agagaagtat taaagtggaa gtttgacagt 600 cgcctggcat acaagcacgt agcccgagag ctgcatccgg agttttacaa agactgctga 660 73 1485 DNA Human immunodeficiency virus type 1 isolate=96ZM651.8; gene=gag 73 atgggtgcga gagcgtcaat attaagaggg ggaaaattag ataaatggga aaaaattagg 60 ctaaggccag ggggaaagaa acgctatatg ataaaacacc tagtatgggc aagcagggag 120 ctggaaagat ttgcgcttaa ccctggcctt ttagaaacat cagaaggctg taaacaaata 180 atgaaacagc tacaaccagc tcttcagaca ggaacggagg aacttagatc attatacaac 240 acagtagcaa ctctctattg tgtacatgaa ggggtagagg tacgagacac caaggaagcc 300 ttagacagga tagaggaaga acaaaacaaa attcagcaaa aaatacagca aaaaacacag 360 caagcggctg acggaaaggt cagtcaaaat tatcctatag tgcagaatct ccaagggcaa 420 atggtacacc agaaactatc acctagaact ttgaatgcat gggtaaaagt aatagaagaa 480 aaagctttta gcccagaggt aatacccatg tttacagcat tatcagaagg agccacccca 540 caagatttaa acaccatgtt aaatacagtg gggggacatc aagcagccat gcaaatgtta 600 aaagatacta tcaatgagga ggctgcagaa tgggatagat tacatccagt gcatgcaggg 660 cctattgcac caggccaaat gagagaacca aggggaagtg atatagcagg aactactagt 720 accctccaag aacagatagc atggatgaca agtaatcccc ctattccagt gggagacatc 780 tataaaagat ggataattct ggggttaaat aaaatagtaa gaatgtatag ccctgtcagc 840 attttggaca taaaacaagg gccaaaggaa ccctttagag actatgtaga ccggttcttc 900 aaaactttaa gagctgaaca ggctacacaa gaagtaaaaa attggatgac agacaccttg 960 ttggtccaaa atgcaaaccc agattgcaag accattttaa aagcattagg accaggggct 1020 acattagaag aaatgatgac agcatgtcaa ggagtgggag gacctagcca caaagcaaga 1080 gtgttggctg aggcaatgag ccaaacaaat agtgtaaaca tactgatgca gaaaagcaat 1140 tttaaaggaa ataaaagaat ggttaaatgt tttaactgtg gtaaggaagg gcacatagcc 1200 agaaattgca gggcccctag gaaaaagggc tgttggaaat gtggaaagga gggacaccaa 1260 atgaaagact gtactgagag gcaggctaat tttttaggga aaatttggcc ttcccacaag 1320 ggaaggccag ggaatttcct tcagaacagg ccagagccaa cagccccacc agcagagagc 1380 ttcaggttcg aggagacaac ccccgctccg aagcaggagt cgaaagacag ggaagcctta 1440 acttccctca aatcactctt tggcagcgac cccttgtctc aataa 1485 74 3000 DNA Human immunodeficiency virus type 1 isolate=96ZM651.8; gene=pol 74 ttttttaggg aaaatttggc cttcccacaa gggaaggcca gggaatttcc ttcagaacag 60 gccagagcca acagccccac cagcagagag cttcaggttc gaggagacaa cccccgctcc 120 gaagcaggag tcgaaagaca gggaagcctt aacttccctc aaatcactct ttggcagcga 180 ccccttgtct caataaaggt agggggccaa ataaaggagg ctctcttaga cacgggagca 240 ggtgatacag tattagaaga aataaatttg ccaggcaaat ggaaaccaaa aatgatagga 300 ggaattggag gctttatcga agtaagacaa tatgatcaaa tacctatgga aatttgtgga 360 aaaaaggcta taggtacagt attagtagga cctacacctg tcaacataat tggaagaaat 420 atgttgactc agcttggatg cacactaaat tttccaatta gtcctattga aactgtacca 480 gtaaaattaa agccaggaat ggatggccca aaggttaaac aatggccatt gacagaagag 540 aaaataaaag ctttaacagc aatttgtgaa gaaatggaga aggaaggaaa aattacaaaa 600 attgggcctg aaaatccata taacactcca gtatttgcca taaaaaagaa ggacagtact 660 aagtggcgaa aattagtaga tttcagggaa ctcaataaaa gaactcaaga cttttgggaa 720 gttcaattag gaataccaca cccagcaggg ttaaaaaaga aaaaatcagt gacagtactg 780 gatgtggggg atgcatattt ttcagttcct ttagatgaaa gcttcaggaa atatactgca 840 ttcaccatac ctagtacaaa caatgaaaca ccagggatta gatatcaata taatgtgctt 900 ccacagggat ggaaaggatc accagcaata ttccagagta gcatgacaaa aatcttagag 960 cccttcaggg cacaaaatcc agacatagtc atctatcaat atatggatga cctgtatgta 1020 ggatctgact tagaaatagg gcaacataga gcaaaaatag aagagttaag agaacatcta 1080 ttaaagtggg gatttaccac accagacaag aaacatcaga aagaaccccc atttctttgg 1140 atggggtatg aactccatcc tgacaaatgg acagtacagc ctatacagct ggcagaaaaa 1200 gatagctgga ctgttaatga tatacagaag ttagtgggaa aattaaactg ggcaagtcag 1260 atttacgcag ggattaaagt aaggcaactt tgtaaactcc ttaggggagc caaagcacta 1320 acagacatag taccactaac tgaagaagca gaattagaat tggcagagaa caaggaaatt 1380 ttaaaagaac cagtacatgg ggtatattat gacccatcaa aagacttgat agctgaaata 1440 cagaaacaag ggcatgacca atggacatat caaatttacc aggaaccatt caaaaatctg 1500 aaaacaggga agtatgcaaa aatgaggaca gcccacacta atgatgtaaa acagttaaca 1560 gaggcagtgc aaaaaatagc cctggagagc atagtaatat ggggaaagat tcctaaattt 1620 agactaccca tccaaaaaga aacatgggaa acatggtgga cagactattg gcaagccacc 1680 tggattcctg agtgggagtt tgttaatacc cctctcttag taaaattatg gtaccagctg 1740 gagaaagaac ccatagtagg agcagaaacc ttctatgtag atggagcagc caatagggaa 1800 actaaattag gaaaagcagg gtatattact gacagaggaa ggcaaaaaat tgttactcta 1860 actgaaacaa caaatcagaa gactgaatta caagcaattt acctagcttt gcaagattca 1920 ggatcagaag taaacatagt aactgactca cagtatgcgt taggaatcat tcaagcacat 1980 ccagataaga gtgaatcaga gttagtcaac caaataatag aacaattaat aaagaaggaa 2040 agggtctacc tgtcatgggt accagcacat aaaggaattg gaggtaatga acaggtagat 2100 aaattagtaa gcaagggaat caggaaagtg ctgtttctag atggaataga caaggctcaa 2160 gaagagcatg aaaaatatca caacaattgg agagcaatgg ctagtgaatt taatctacca 2220 ccagtagtag caaaagaaat agtagctagt tgtgataaat gtcagcaaaa aggggaagcc 2280 acacatggac aagtagactg tagtccaggg atatggcaat tagactgtac acatttagaa 2340 ggaaaaatca tcctggtagc agtccatgta gccagtggct acatagaagc agaggttatc 2400 ccagcagaaa caggacaaga aacagcatac tatatattaa aattagcagg aagatggcca 2460 gtcaaagtaa tacatacaga caatggtagc aattttacca gtgctgcagt taaggcagcc 2520 tgttggtggg caggtatcaa acaagaattt ggaattccct acaatccaca aagtcaggga 2580 gtagtagaat ccatgaataa agaattaaag aaaatcatag ggcaggtaag agatcaggct 2640 gagcatctta aaacagcagt acaaatggca gtattcattc acaattttaa aagaaaaagg 2700 gggattgggg ggtacagtgc aggggaaaga ataatagaca taatagcaac agacatacaa 2760 accaaagaac tacaaaaaca aattataaac attcaaaaat ttcgggttta ttacagagac 2820 agcagagacc ccatttggaa aggaccagcc aaactactct ggaaaggtga aggggcagta 2880 gtaatacaag ataatagtga cataaaagtg gtaccaagga ggaaagcaaa aatcattagg 2940 gactatggaa aacagatggc aggcgctgat tgtgtggcag gtagacagga tgaggattag 3000 75 579 DNA Human immunodeficiency virus type 1 isolate=96ZM651.8; gene=vif 75 atggaaaaca gatggcaggc gctgattgtg tggcaggtag acaggatgag gattagaaca 60 tggaatagtt tagtaaagca ccatatgtat atttcacgga aagctaatgg atggttttac 120 agacatcatt atgaaagcag acatccaagg gtaagttcag aagtacatat cccattaggg 180 gatgctaaat tagtaataaa aacatattgg ggtttgcaaa caggagaaag agattggcat 240 ttgggtcatg gagtctccat agaatggaga ttgagaagat atagcacaca agtagaccct 300 ggcctggcag accagctaat tcatatgcac tattttgatt gttttgcaga ctctgccata 360 agaaaagcca tattaggaca catagttatt cctaggtgtg actatcaagc aggacataat 420 aaggtaggat ctctgcaata cttggcactg acagcattga taaaaccaaa aaagagaaag 480 ccacctctgc ctagtgttag gaaattagta gaggatagat ggaacaattc ccagaagacc 540 aagggccgca gagggaacca tacagtgagt ggacactag 579 76 291 DNA Human immunodeficiency virus type 1 isolate=96ZM651.8; gene=vpr 76 atggaacaat tcccagaaga ccaagggccg cagagggaac catacagtga gtggacacta 60 gagattctag aggaactcaa gcaggaagct gtcagacact ttcctagacc atggctccat 120 agcttaggac aacatatcta tgaaacttat ggggatactt ggactggagt cgaggctata 180 ataagaatac tgcaacaact actgtttatt catttcagaa ttgggtgcca gcacagcaga 240 ataggcatgg ttcgacagag aagagcgaga aatggagcca gtagatccta g 291 77 2666 DNA Human immunodeficiency virus type 1 isolate=96ZM651.8; gene=tat 77 atggagccag tagatcctag catagagccc tggaaccatc caggaagtca gcctaaaact 60 gcttgtaata agtgttattg caaacgctgt agctatcatt gtctagtttg ctttcagaca 120 aaaggcttag gcatttcata tggcaggaag aagcggagac agcgacgcag cactcctcct 180 agcagcgagg accatcaaga tcctatatca aagcagtaag tatatgtaat gttagattta 240 ctagcaagag taaattatag agtaggagta ggagcattga tagtagcact actcatagca 300 atagttgtgt ggaccatagc atatatagaa tataggaagc tgttaagaca aagaaaaata 360 gactggttaa ttaaaagaat tagggaaaga gcagaagaca gtggcaatga gagtgaggga 420 gatactgagg aattggcaac gatggtggac atggggcatc ttaggctttt ggatgttaat 480 gatttgtaat gtgtggggga acttgtgggt cacagtctat tatggggtac ctgtgtggaa 540 agaagcaaaa actactctat tctgtgcatc agatgctaaa tcatatgaga aagaagtgca 600 taatgtctgg gctacacatg cctgtgtacc cacagacccc aacccacaag aaatagtttt 660 gggaaatgta acagaaaatt ttaacatgtg gaaaaatgac atggtggatc agatgcatga 720 ggatataatc agtttatggg atcaaagcct aaagccatgt gtaaagttga ccccactctg 780 tgtcacttta aattgtacag aggttaatgt taccagaaat gttaataata gcgtggttaa 840 taataccaca aatgttaata atagcatgaa tggagacatg aaaaattgct ctttcaacat 900 aaccacagaa ctaaaagata agaaaaagaa tgtgtatgca cttttttata aacttgatat 960 agtatcactt aatgagactg acgactctga gactggcaac tctagtaaat attatagatt 1020 aataaattgt aatacctcag ccctaacaca agcctgtcca aaggtctctt ttgacccaat 1080 tcctatacat tattgtgctc cagctggtta tgcgattcta aagtgtaata ataagacatt 1140 caatgggaca ggaccatgcc ataatgtcag cacagtacaa tgtacacatg gaattaagcc 1200 agtggtatca actcaactac tgttaaatgg tagcctagca gaagaaggga taataattag 1260 atctgaaaat ctgacaaaca atgtcaaaac aataatagta catcttaata gatctataga 1320 aattgtgtgt gtaagaccca acaataatac aagacaaagt ataagaatag gaccaggaca 1380 aacattctat gcaacaggag acataatagg agacataaga caagcacatt gtaacattag 1440 taggactaac tggactaaga ctttacgaga ggtaaggaac aaattaagag aacacttccc 1500 taataaaaac ataacattta aaccatcctc aggaggggac ctagaaatta caacacatag 1560 ctttaattgt agaggagaat ttttctattg caatacatcg ggcctgttta gtataaatta 1620 tacagaaaat aatacagatg gtacacccat cacactccca tgcagaataa gacaaattat 1680 aaatatgtgg caggaagtag gacgagcaat gtacgcccct cccattgaag gaaacatagc 1740 atgtaaatca gatatcacag ggctactatt ggttcgggat ggaggaagca caaatgatag 1800 cacaaataat aacacagaga tattcagacc tgcaggagga gatatgaggg acaattggag 1860 gagtgaattg tataagtata aagtggtaga aattaagcca ttgggaatag cacccactga 1920 ggcaaaaagg agagtggtgg agagagaaaa aagagcagtg ggaataggag ctgtgttcct 1980 tgggttcttg ggagcagcag gaagcactat gggcgcagcg tcaataacgc tgacggcaca 2040 ggccagacaa gtgttgtctg gtatagtgca acagcaaagc aatttgctga gggctataga 2100 ggcgcaacag catctgttgc aactcacggt ctggggcatt aagcagctcc agacaagagt 2160 cctggctata gaaagatacc taaaggatca acagctccta ggactttggg gctgctctgg 2220 aaaactcatc tgcaccactg ctgtgccttg gaacatcagt tggagtaata aatctaaaac 2280 agatatttgg gataacatga cctggatgca gtgggataga gaaattagta attacacaaa 2340 cacaatatac aggttgcttg aggactcgca gagccagcag gagcaaaatg aaaaagattt 2400 attagcattg gacagttgga acaatctgtg gaattggttt gacataacaa aatggctgtg 2460 gtatataaaa atatttataa tgatagtagg aggcttaata ggtttgagaa taatttttgc 2520 tgtactctct atagtgaata gagttaggca gggatactca cctttgtcgt ttcagaccct 2580 tatcccgaac ccaagggaac ccgacaggcc aggaagaatc gaagaagaag gtggagagca 2640 agacaaagag agatccgtgc gattag 2666 78 2684 DNA Human immunodeficiency virus type 1 isolate=96ZM651.8; gene=rev 78 atggcaggaa gaagcggaga cagcgacgca gcactcctcc tagcagcgag gaccatcaag 60 atcctatatc aaagcagtaa gtatatgtaa tgttagattt actagcaaga gtaaattata 120 gagtaggagt aggagcattg atagtagcac tactcatagc aatagttgtg tggaccatag 180 catatataga atataggaag ctgttaagac aaagaaaaat agactggtta attaaaagaa 240 ttagggaaag agcagaagac agtggcaatg agagtgaggg agatactgag gaattggcaa 300 cgatggtgga catggggcat cttaggcttt tggatgttaa tgatttgtaa tgtgtggggg 360 aacttgtggg tcacagtcta ttatggggta cctgtgtgga aagaagcaaa aactactcta 420 ttctgtgcat cagatgctaa atcatatgag aaagaagtgc ataatgtctg ggctacacat 480 gcctgtgtac ccacagaccc caacccacaa gaaatagttt tgggaaatgt aacagaaaat 540 tttaacatgt ggaaaaatga catggtggat cagatgcatg aggatataat cagtttatgg 600 gatcaaagcc taaagccatg tgtaaagttg accccactct gtgtcacttt aaattgtaca 660 gaggttaatg ttaccagaaa tgttaataat agcgtggtta ataataccac aaatgttaat 720 aatagcatga atggagacat gaaaaattgc tctttcaaca taaccacaga actaaaagat 780 aagaaaaaga atgtgtatgc acttttttat aaacttgata tagtatcact taatgagact 840 gacgactctg agactggcaa ctctagtaaa tattatagat taataaattg taatacctca 900 gccctaacac aagcctgtcc aaaggtctct tttgacccaa ttcctataca ttattgtgct 960 ccagctggtt atgcgattct aaagtgtaat aataagacat tcaatgggac aggaccatgc 1020 cataatgtca gcacagtaca atgtacacat ggaattaagc cagtggtatc aactcaacta 1080 ctgttaaatg gtagcctagc agaagaaggg ataataatta gatctgaaaa tctgacaaac 1140 aatgtcaaaa caataatagt acatcttaat agatctatag aaattgtgtg tgtaagaccc 1200 aacaataata caagacaaag tataagaata ggaccaggac aaacattcta tgcaacagga 1260 gacataatag gagacataag acaagcacat tgtaacatta gtaggactaa ctggactaag 1320 actttacgag aggtaaggaa caaattaaga gaacacttcc ctaataaaaa cataacattt 1380 aaaccatcct caggagggga cctagaaatt acaacacata gctttaattg tagaggagaa 1440 tttttctatt gcaatacatc gggcctgttt agtataaatt atacagaaaa taatacagat 1500 ggtacaccca tcacactccc atgcagaata agacaaatta taaatatgtg gcaggaagta 1560 ggacgagcaa tgtacgcccc tcccattgaa ggaaacatag catgtaaatc agatatcaca 1620 gggctactat tggttcggga tggaggaagc acaaatgata gcacaaataa taacacagag 1680 atattcagac ctgcaggagg agatatgagg gacaattgga ggagtgaatt gtataagtat 1740 aaagtggtag aaattaagcc attgggaata gcacccactg aggcaaaaag gagagtggtg 1800 gagagagaaa aaagagcagt gggaatagga gctgtgttcc ttgggttctt gggagcagca 1860 ggaagcacta tgggcgcagc gtcaataacg ctgacggcac aggccagaca agtgttgtct 1920 ggtatagtgc aacagcaaag caatttgctg agggctatag aggcgcaaca gcatctgttg 1980 caactcacgg tctggggcat taagcagctc cagacaagag tcctggctat agaaagatac 2040 ctaaaggatc aacagctcct aggactttgg ggctgctctg gaaaactcat ctgcaccact 2100 gctgtgcctt ggaacatcag ttggagtaat aaatctaaaa cagatatttg ggataacatg 2160 acctggatgc agtgggatag agaaattagt aattacacaa acacaatata caggttgctt 2220 gaggactcgc agagccagca ggagcaaaat gaaaaagatt tattagcatt ggacagttgg 2280 aacaatctgt ggaattggtt tgacataaca aaatggctgt ggtatataaa aatatttata 2340 atgatagtag gaggcttaat aggtttgaga ataatttttg ctgtactctc tatagtgaat 2400 agagttaggc agggatactc acctttgtcg tttcagaccc ttatcccgaa cccaagggaa 2460 cccgacaggc caggaagaat cgaagaagaa ggtggagagc aagacaaaga gagatccgtg 2520 cgattagtga gcggattctt agcacttgcc tgggacgacc tacggagcct gtgcctcttc 2580 agctaccacc gattgagaga cttcatattg gtgacagcga gagcggtgga gcttctgaga 2640 cgcagcagtc tcaagggact acagaggggg tgggaagccc ttaa 2684 79 261 DNA Human immunodeficiency virus type 1 isolate=96ZM651.8; gene=vpu 79 atgttagatt tactagcaag agtaaattat agagtaggag taggagcatt gatagtagca 60 ctactcatag caatagttgt gtggaccata gcatatatag aatataggaa gctgttaaga 120 caaagaaaaa tagactggtt aattaaaaga attagggaaa gagcagaaga cagtggcaat 180 gagagtgagg gagatactga ggaattggca acgatggtgg acatggggca tcttaggctt 240 ttggatgtta atgatttgta a 261 80 2607 DNA Human immunodeficiency virus type 1 isolate=96ZM651.8; gene=env 80 atgagagtga gggagatact gaggaattgg caacgatggt ggacatgggg catcttaggc 60 ttttggatgt taatgatttg taatgtgtgg gggaacttgt gggtcacagt ctattatggg 120 gtacctgtgt ggaaagaagc aaaaactact ctattctgtg catcagatgc taaatcatat 180 gagaaagaag tgcataatgt ctgggctaca catgcctgtg tacccacaga ccccaaccca 240 caagaaatag ttttgggaaa tgtaacagaa aattttaaca tgtggaaaaa tgacatggtg 300 gatcagatgc atgaggatat aatcagttta tgggatcaaa gcctaaagcc atgtgtaaag 360 ttgaccccac tctgtgtcac tttaaattgt acagaggtta atgttaccag aaatgttaat 420 aatagcgtgg ttaataatac cacaaatgtt aataatagca tgaatggaga catgaaaaat 480 tgctctttca acataaccac agaactaaaa gataagaaaa agaatgtgta tgcacttttt 540 tataaacttg atatagtatc acttaatgag actgacgact ctgagactgg caactctagt 600 aaatattata gattaataaa ttgtaatacc tcagccctaa cacaagcctg tccaaaggtc 660 tcttttgacc caattcctat acattattgt gctccagctg gttatgcgat tctaaagtgt 720 aataataaga cattcaatgg gacaggacca tgccataatg tcagcacagt acaatgtaca 780 catggaatta agccagtggt atcaactcaa ctactgttaa atggtagcct agcagaagaa 840 gggataataa ttagatctga aaatctgaca aacaatgtca aaacaataat agtacatctt 900 aatagatcta tagaaattgt gtgtgtaaga cccaacaata atacaagaca aagtataaga 960 ataggaccag gacaaacatt ctatgcaaca ggagacataa taggagacat aagacaagca 1020 cattgtaaca ttagtaggac taactggact aagactttac gagaggtaag gaacaaatta 1080 agagaacact tccctaataa aaacataaca tttaaaccat cctcaggagg ggacctagaa 1140 attacaacac atagctttaa ttgtagagga gaatttttct attgcaatac atcgggcctg 1200 tttagtataa attatacaga aaataataca gatggtacac ccatcacact cccatgcaga 1260 ataagacaaa ttataaatat gtggcaggaa gtaggacgag caatgtacgc ccctcccatt 1320 gaaggaaaca tagcatgtaa atcagatatc acagggctac tattggttcg ggatggagga 1380 agcacaaatg atagcacaaa taataacaca gagatattca gacctgcagg aggagatatg 1440 agggacaatt ggaggagtga attgtataag tataaagtgg tagaaattaa gccattggga 1500 atagcaccca ctgaggcaaa aaggagagtg gtggagagag aaaaaagagc agtgggaata 1560 ggagctgtgt tccttgggtt cttgggagca gcaggaagca ctatgggcgc agcgtcaata 1620 acgctgacgg cacaggccag acaagtgttg tctggtatag tgcaacagca aagcaatttg 1680 ctgagggcta tagaggcgca acagcatctg ttgcaactca cggtctgggg cattaagcag 1740 ctccagacaa gagtcctggc tatagaaaga tacctaaagg atcaacagct cctaggactt 1800 tggggctgct ctggaaaact catctgcacc actgctgtgc cttggaacat cagttggagt 1860 aataaatcta aaacagatat ttgggataac atgacctgga tgcagtggga tagagaaatt 1920 agtaattaca caaacacaat atacaggttg cttgaggact cgcagagcca gcaggagcaa 1980 aatgaaaaag atttattagc attggacagt tggaacaatc tgtggaattg gtttgacata 2040 acaaaatggc tgtggtatat aaaaatattt ataatgatag taggaggctt aataggtttg 2100 agaataattt ttgctgtact ctctatagtg aatagagtta ggcagggata ctcacctttg 2160 tcgtttcaga cccttatccc gaacccaagg gaacccgaca ggccaggaag aatcgaagaa 2220 gaaggtggag agcaagacaa agagagatcc gtgcgattag tgagcggatt cttagcactt 2280 gcctgggacg acctacggag cctgtgcctc ttcagctacc accgattgag agacttcata 2340 ttggtgacag cgagagcggt ggagcttctg agacgcagca gtctcaaggg actacagagg 2400 gggtgggaag cccttaagta tctgggaagt cttgtgcagt attggggtct ggagctaaaa 2460 aagagtgcta ttagtctact tgataccata gcaatagcag tagctgaagg aacagatagg 2520 attatagaat taatacaagg aatttgtaga gctatccgca acgtacctag aagaataaga 2580 cagggctttg aaacagcttt gctataa 2607 81 621 DNA Human immunodeficiency virus type 1 nef 81 atggggggca agtggtcaaa aagcagtata gttggatggc ctgctgtaag agagagaata 60 agaagaactg agccagcagc agagggagta ggagcagcgt ctcaagactt agataaatat 120 ggagcactta caagcagcaa cacaagtacc actaatgctg cttgtgcctg gctggaagca 180 caagaggagg aagaagttgg ctttccagtc agacctcagg tgcctttaag accaatgact 240 tataaggcag cagtcgatct cagcttcttt ttaaaagaaa aggggggact ggaagggtta 300 atttactcta agaaaaggca agaaatcctt gatttgtggg tctatcacac acaaggcttc 360 ttccctgact ggcaaaacta cacaccggga ccaggggtca gatatccact gacctttgga 420 tggtgcttca agctagtgcc agttgatcca ggggaagtag aagaggccaa cgaaggagaa 480 aacaactgtc tgctacaccc tatgagccag caaggaatgg atgatgatca cagagaagta 540 ttaaagtgga agtttgacag tcacctagca cataaacaca tggcccgaga gctacatccg 600 gagtattaca aagactgctg a 621 82 1496 DNA Human immunodeficiency virus type 1 isolate=96ZM751.3; gene=gag 82 atgggtgcga gagcgtcaat attaagaggc ggaaaattag atgaatggga aagaattagg 60 ttaaggccag ggggaaaaaa gcactatatg atgaaacact taatatgggc aagcagggag 120 ctggaaagat ttgcacttaa ccctggcctt ttagagacat cagaaggctg taaacaaata 180 atacaacagc tacaaccagc tctccagaca ggaacagagg aacttaggtc attatataat 240 acagtagcaa ctctctattg tgtacatgaa aagataaagg tacgagacac caaggaagcc 300 ctagacaaga tagaggaaga acaaaacaaa agtcaacaaa aaatacaaaa aacagaagcg 360 actggcggaa aggtcagtca aaattatcct atagtgcaga atctccaagg gcaaatggta 420 caccaggcta tatcacctag aactttgaat gcatgggtaa aagtaataga ggagaagggt 480 ttcaacccag aggtaatacc catgtttaca gcattatcag aaggagccac cccacaagat 540 ctaaacacca tgttaaatac agtgggggga catcaagcag ccatgcaaat gttaaaagat 600 accatcaatg aggaagctgc agaatgggat aggttacatc cagtacatgc agggcctatt 660 gcaccaggcc aaataagaga accaagggga agtgacatag caggaactac tggtaccctt 720 caggaacaaa tagcatggat gacaaataac ccacctattc cagtgggaga catctataaa 780 agatggataa ttctggggtt aaataaaata gtaagaatgt acagccctgt cagcattctg 840 gacataaaac aaggaccaaa ggaacccttt agggactatg tagatcggtt ctttaaaact 900 ttaagagctg aacaagctac acaagatgta aaaattggat gacagacacc ttgttggttc 960 aaaatgcgaa cccagattgt aagaccattt taagggcatt aggaccaggg gctacattag 1020 aagaaatgat gacagcatgt cagggagtgg ggggacctgg ccacaaagca agagttttgg 1080 ctgaagcaat gagccaagta aacaatacaa acataatgat gcagaaaagc aattttaaag 1140 gccctaaaag aattgttaaa tgtttcaact gtggcaggga agggcatata gccaggaatt 1200 gcagggctcc tgggaaaaaa ggctgttgga aatgtggaaa ggaaggacac caaatgaaag 1260 actgtactga gagacaggct aattttttag ggaaaatttg gccttcccag aaggggaggc 1320 cggggaactt ccttcagaac agaccagagc caacagcccc accagctcca acagccccac 1380 cagcagagag cttcaggttc gaggagacaa cccctgcccc gaggcaggag cagaaagaca 1440 aggaaccctt aactgccctc aaatcactct ttggcagcga ccccttgtct caataa 1496 83 3017 DNA Human immunodeficiency virus type 1 isolate=96AM751.3; gene=pol 83 ttttttaggg aaaatttggc cttcccagaa ggggaggccg gggaacttcc ttcagaacag 60 accagagcca acagccccac cagctccaac agccccacca gcagagagct tcaggttcga 120 ggagacaacc cctgccccga ggcaggagca gaaagacaag gaacccttaa ctgccctcaa 180 atcactcttt ggcagcgacc ccttgtctca ataaaagtag ggggtcagat aaaggaggct 240 ctcttggata caggagcaga tgatacagta ttagaagaaa taaatttgcc aggaaaatgg 300 aaaccaaaaa tgataggagg aattggaggt tttatcaaag taagacagta tgatcaaata 360 cttatagaaa tttgtggaaa aaaggctata ggtacagtat tagtaggacc tacacctgtc 420 aacataattg ggagaaatat gttgacccag cttggctgca cactaaattt tccaattagt 480 cctattgaaa ctgtaccagt aaaattaaag ccaggaatgg atggcccaag ggtcaaacaa 540 tggccattga cagaagaaaa aataaaagca ttaacagcaa tttgtgaaga aatggaaaag 600 gaaggaaaaa ttacaaaaat tggccctgag aatccatata acactccagt atttgccata 660 aaaaagaagg acagtactaa gtggagaaaa ttagtagatt tcagggaact caataaaaga 720 actcaggact tttgggaagt tcaattagga ataccacacc cagcggggtt aaaaaagaaa 780 aagtcagtga cagtactgga tgtgggggat gcgtattttt cagttccttt agatgaaggc 840 ttcaggaaat atactgcatt caccatacct agtataaaca atgaaacacc tgggattaga 900 tatcaatata atgtgcttcc acagggatgg aaaggatcac catcaatatt ccagagtagc 960 atgataaaaa tcttagagcc ctttaggaca caaaacccag aaatagttat ctatcaatat 1020 atggatgact tgtatgtagg atctgattta gaaatagggc aacacagagc aaaaatagag 1080 gagttaagag aacacctatt gagatgggga tttactacac cagacaagaa gcatcagaaa 1140 gagcccccat ttctttggat ggggtatgaa ctccatcctg acaaatggac agtacagcct 1200 ataaagctgc cagaaaagga gagctggact gtcaatgata tacagaagtt agtgggaaaa 1260 ttaaactggc aagtcagatt tacgcaggga ttaaagtaag gcaactgtgt aaactcctta 1320 ggggagccaa agcactaaca gacatagtac cattgactga agaggcagaa ttagaattgg 1380 cagagagcag ggaaattcta aaagaaccag tacatggagt atattatgac ccatcaaaag 1440 acttaatagc tgaaatacag aaacaagggc atgaccaatg gacatatcaa gtttaccaag 1500 aaccattcaa aaatctgaaa acaggaaagt atgcaaaaat gaggactgcc cacactaatg 1560 atgtaaaaca gttaacagag gcggtgcaaa aaatagccat ggaaagcata gtaatatggg 1620 gaaagattcc taaatttagg ctacccattc aaaaagaaac atgggagaca tggtggacag 1680 actattggca agccacctgg attcctgagt gggagtttgt taatactccc cccctagtaa 1740 aattatggta ccagctggag aaagaaccca tagcaggagc agaaacttac tatgtagatg 1800 gagcagccaa tagggaaact aaaataggaa aagcagggta tgttactgac agaggaaggc 1860 aaaaaattgt tactctaact gaaacaacaa atcaaaagac tgaattacaa gcaattcagt 1920 tagctttgca ggattcagga tcagaagtaa acatagtaac agactcacag tatgcattag 1980 gaatcatcca agcacaacca gataagagtg aatcagaatt agtcaatcaa ataatagaac 2040 agttgataaa aaaggaaagg gtttacctgt catgggtacc agcacacaaa ggaattggag 2100 gaaatgaaca agtagataaa ttggtaagta gtggaatcag gaaagtgctg tttctagatg 2160 gaatagataa ggctcaagaa gagcatgaaa aatatcacag caattggaga gcaatggcta 2220 gtgagtttaa tctgccaccc atagtagcaa aagaaatagt agccagctgt gataaatgtc 2280 agctaaaagg ggaagccata catggacaag tagactgtag tccaggaata tggcaattag 2340 attgtaccca tttagaagga aaagtcatct tggtagcagt ccatgtagcc agtggttaca 2400 tagaagcaga ggtcacccca gcggaaacag gacaagaaac agcacttttc atactaaaat 2460 tagcaggaag atggccagtc aaagtagtac atacagacaa tggcagtaat ttcaccagtg 2520 ctgcagtcaa ggcagcctgt tggtgggcag gtatccacca ggaatttgga attccctaca 2580 atccccaaag tcaaggagta gtagaatcca tgaataaaga attaaagaaa attatagggc 2640 aggtaagaga tcaagctgag caccttaaga cagcagtaca aatggcagta ttcattcaca 2700 attttaaaag aaaagggggg attggggggt acagtgcagg ggaaagaata atagacataa 2760 tagcaacaga catacaaact agagaattac aaaaacaaat tataaaaatt caaaattttc 2820 gggtttatta cagagacagc agagacccta tttggaaagg accagccaaa ctactctgga 2880 aaggtgaagg ggcagtagta atacaagata atagtgacat aaaggtaata ccaaggagga 2940 aagcaaaaat cattagggac tatggaaaac agatggcagg tactgatagt gtggcaggta 3000 gacaggatga agattag 3017 84 579 DNA Human immunodeficiency virus type 1 isolate=96ZM751.3; gene=vif 84 atggaaaaca gatggcaggt actgatagtg tggcaggtag acaggatgaa gattagaaca 60 tggaatagtt tagtaaagca ccatatgtat gtttcaaaaa gaactggtag atggttttac 120 agacatcatt atgaaagcag acatccaaaa ataagttcag aagtacacat cccattaggg 180 gatgccaaat tagtaataaa aacatattgg gggctgcatc caggggaaag agaatggcat 240 ttgggtcatg gagtctccat agaatggaga ttgagaagat acagcacaca agtagaccct 300 ggcctggcag accagctaat tcatatgcat tattttaatt gttttgcaga ctctgccata 360 agaaaagccc tactaggaca tatagttatt cctaggtgtg attatcaagc aggacataat 420 aaggtaggat ccctacaata cttggcactg acagcattga taaaaccaaa aaagataaag 480 ccacctttac ctagtgttag gaaattagta gaggatagat ggaacaagcc ccagaaaacc 540 aagggccgca gagggaacca tataatgaat gggcactag 579 85 291 DNA Human immunodeficiency virus type 1 isolate=96ZM751.3; gene=vpr 85 atggaacaag ccccagaaaa ccaagggccg cagagggaac catataatga atgggcacta 60 gagcttttag aggagctcaa gcaggaagct gtcagacact ttcctagaac atggctccat 120 aacttaggac aacatatcta ccaaacctac ggggatactt ggacgggggt tgaagctcta 180 ataagaatac tgcaacaact actgtttatt catttcagaa ttggatgcca acatagcaga 240 ataggcatta tgcgacagag aagagcaaga aatggagcca gtagatccta g 291 86 2646 DNA Human immunodeficiency virus type 1 isolate=96AM751.3; gene=tat 86 atggagccag tagatcctag actagagccc tggaatcatc caggaagtca acctaaaact 60 ccttgtaata agtgttattg taaacactgt agctatcatt gtctagtttg ctttcagaca 120 aaaggcttag gcatttccta tggcaggaag aagcggagac aacgacgaag cgctcctcca 180 agcagtgagg atcatcaaaa tcctatatca aagcagtaag tacaaagtaa tagatgtaat 240 gttaaattta gaagcaagag tagattatag aataggagta ggagcattaa tagcagcact 300 aatcatagca atagctgtgt ggatcatagt atatatagaa tatagaaaat tgtcaagaca 360 aagaaaaata gaccggttaa ttaaaagaat tagagaaagg gcagaagaca gtggcaatga 420 gagtgaaggg gataatgagg aattggcaac aatggtggat atggggcatc ttaggctttt 480 ggatgctatt gatgtgtaat gcaatgggga aattgtgggt cacagtctac tatggggtac 540 ctgtgtggaa agaagcaaaa actactttat tttgtgcatc agatgctaaa gcatatgaga 600 cagaagtgca taatgtttgg gctacacatg cctgtgtacc cacagacccc aacccacaag 660 aaatggtttt ggaaaatgta acagaaaagt ttaacatgtg ggaaaataac atggtggatc 720 agatgcatga ggatataatc agtttatggg accaaagcct aaagccatgt gtaaagttga 780 ccccactctg tgtcacttta aactgtactg ctaatataac caacaatgct aatataacca 840 acaatgctaa tataaccaac tataataatg aaactgacat gagaaattgc tctttcaata 900 taaccacaga attaagagat aagaggaggc aagtagatgc actcttttat aaacttgata 960 tagtaccaat taatgagaat tccagtgaat atagattaat aaattgtaat acctcggcca 1020 taacacaagc atgtccaaag gttacttttg acccaatccc tatacattat tgtgctccag 1080 ctggttatgc gattctaaag tgtaacaata agacattcaa tggaacagga ccatgcaata 1140 atgtcagcac agtacaatgt acacatggaa ttaagccagt agtatcaact caattactgt 1200 taaatggtag tctagcagaa gaagagataa taattagatc taaaaatatg acagacaatg 1260 ccaaaataat aatagtacat cttaatgaat ctgtagaaat tgtgtgtaca agacccaaca 1320 ataatacaag gaaaagtgtg aggataggac caggacaaac attctatgca acaggagaaa 1380 taataggaaa tataagacaa gcatattgta acatcagtga aggcaaatgg aataacactc 1440 tacaaagggt aggtgaaaaa ttaagaaaat acttccctaa taaaacaata agctttgcac 1500 catcctcagg aggggaccta gaaattacaa cacatagctt taattgtaga ggagaatttt 1560 tctattgcaa tacatcaaaa ctgtttaatg gtacgtttaa tggtacaaac acttctaatg 1620 atagaagtaa ttcgaccatt acgcttcaat gcagaataaa acaaattaca aacatgtggc 1680 agggggtagg acaagcaatg tatgctcctc caattaaagg aaacataaca tgtaaatcaa 1740 atatcacagg actactatta acacgtgatg gagggacaaa tgacacagag acaccagaga 1800 cattcagacc tggaggagga gacatgaagg acaattggag aagtgaatta tataaatata 1860 aagtggtaga aattaagcca ttaggagtag cacccactaa ggcacgaagg agagtggtgg 1920 agagagaaaa aagagcagta ggaataggag ctgtgttcct tgggttcttg ggagcagcag 1980 gaagcactat gggcgcagca tcaataacgc tgacggtaca ggtcagacaa ttattgtctg 2040 gtatagtgca acagcaaagc aatttgctga gggctataga ggcgcaacag cacatgttgc 2100 aactcacagt ctggggcatt aagcagctcc aggcaagagt cttggctata gaaagatacc 2160 taaaggatca acagctccta gggatttggg gctgctctgg aaaactcatc tgcaccactg 2220 ctgtgccttg gaactctagt tggagcaaca aatctgaacg ggagatttgg gataacatga 2280 cctggatgca gtgggataga gaaattaata attacacaga aacaatatat aggttgcttg 2340 aagtctcgca aaaccagcag gaaaataatg aaagggattt actagcattg gacagttgaa 2400 aaaatctgtg gaattggttt aatataacaa attggctgtg gtatataaaa atattcataa 2460 tgataatagg aggcttgata ggtttaagaa taatttttgc tgtgctctct atagtaaata 2520 gagttaggca ggggtactca cctttgtcgt tgcagaccct tatcccaacc ccgagggaac 2580 cagacaggct cggaagaatc gaagaagaag gtggagagca agacagagac agatcaattc 2640 gattag 2646 87 2631 DNA Human immunodeficiency virus type 1 isolate=96ZM751.3; gene=rev 87 atggcaggaa gaagcggaga caacgacgaa gcgctcctcc aagcagtgag gatcatcaaa 60 atcctatatc aaagcagtaa gtacaaagta atagatgtaa tgttaaattt agaagcaaga 120 gtagattata gaataggagt aggagcatta atagcagcac taatcatagc aatagctgtg 180 tggatcatag tatatataga atatagaaaa ttgtcaagac aaagaaaaat agaccggtta 240 attaaaagaa ttagagaaag ggcagaagac agtggcaatg agagtgaagg ggataatgag 300 gaattggcaa caatggtgga tatggggcat cttaggcttt tggatgctat tgatgtgtaa 360 tgcaatgggg aaattgtggg tcacagtcta ctatggggta cctgtgtgga aagaagcaaa 420 aactacttta ttttgtgcat cagatgctaa agcatatgag acagaagtgc ataatgtttg 480 ggctacacat gcctgtgtac ccacagaccc caacccacaa gaaatggttt tggaaaatgt 540 aacagaaaag tttaacatgt gggaaaataa catggtggat cagatgcatg aggatataat 600 cagtttatgg gaccaaagcc taaagccatg tgtaaagttg accccactct gtgtcacttt 660 aaactgtact gctaatataa ccaacaatgc taatataacc aacaatgcta atataaccaa 720 ctataataat gaaactgaca tgagaaattg ctctttcaat ataaccacag aattaagaga 780 taagaggagg caagtagatg cactctttta taaacttgat atagtaccaa ttaatgagaa 840 ttccagtgaa tatagattaa taaattgtaa tacctcggcc ataacacaag catgtccaaa 900 ggttactttt gacccaatcc ctatacatta ttgtgctcca gctggttatg cgattctaaa 960 gtgtaacaat aagacattca atggaacagg accatgcaat aatgtcagca cagtacaatg 1020 tacacatgga attaagccag tagtatcaac tcaattactg ttaaatggta gtctagcaga 1080 agaagagata ataattagat ctaaaaatat gacagacaat gccaaaataa taatagtaca 1140 tcttaatgaa tctgtagaaa ttgtgtgtac aagacccaac aataatacaa ggaaaagtgt 1200 gaggatagga ccaggacaaa cattctatgc aacaggagaa ataataggaa atataagaca 1260 agcatattgt aacatcagtg aaggcaaatg gaataacact ctacaaaggg taggtgaaaa 1320 attaagaaaa tacttcccta ataaaacaat aagctttgca ccatcctcag gaggggacct 1380 agaaattaca acacatagct ttaattgtag aggagaattt ttctattgca atacatcaaa 1440 actgtttaat ggtacgttta atggtacaaa cacttctaat gatagaagta attcgaccat 1500 tacgcttcaa tgcagaataa aacaaattac aaacatgtgg cagggggtag gacaagcaat 1560 gtatgctcct ccaattaaag gaaacataac atgtaaatca aatatcacag gactactatt 1620 aacacgtgat ggagggacaa atgacacaga gacaccagag acattcagac ctggaggagg 1680 agacatgaag gacaattgga gaagtgaatt atataaatat aaagtggtag aaattaagcc 1740 attaggagta gcacccacta aggcacgaag gagagtggtg gagagagaaa aaagagcagt 1800 aggaatagga gctgtgttcc ttgggttctt gggagcagca ggaagcacta tgggcgcagc 1860 atcaataacg ctgacggtac aggtcagaca attattgtct ggtatagtgc aacagcaaag 1920 caatttgctg agggctatag aggcgcaaca gcacatgttg caactcacag tctggggcat 1980 taagcagctc caggcaagag tcttggctat agaaagatac ctaaaggatc aacagctcct 2040 agggatttgg ggctgctctg gaaaactcat ctgcaccact gctgtgcctt ggaactctag 2100 ttggagcaac aaatctgaac gggagatttg ggataacatg acctggatgc agtgggatag 2160 agaaattaat aattacacag aaacaatata taggttgctt gaagtctcgc aaaaccagca 2220 ggaaaataat gaaagggatt tactagcatt ggacagttga aaaaatctgt ggaattggtt 2280 taatataaca aattggctgt ggtatataaa aatattcata atgataatag gaggcttgat 2340 aggtttaaga ataatttttg ctgtgctctc tatagtaaat agagttaggc aggggtactc 2400 acctttgtcg ttgcagaccc ttatcccaac cccgagggaa ccagacaggc tcggaagaat 2460 cgaagaagaa ggtggagagc aagacagaga cagatcaatt cgattagtga acggattctt 2520 agcacttgtc tgggacgacc tccggagcct gtgccttttc agctaccacc gcttgagaga 2580 cttcatattg attgcagcga ggggactaca gagggggtgg gaaactctta a 2631 88 261 DNA Human immunodeficiency virus type 1 isolate=96AM751.3; gene=vpu 88 atgttaaatt tagaagcaag agtagattat agaataggag taggagcatt aatagcagca 60 ctaatcatag caatagctgt gtggatcata gtatatatag aatatagaaa attgtcaaga 120 caaagaaaaa tagaccggtt aattaaaaga attagagaaa gggcagaaga cagtggcaat 180 gagagtgaag gggataatga ggaattggca acaatggtgg atatggggca tcttaggctt 240 ttggatgcta ttgatgtgta a 261 89 2544 DNA Human immunodeficiency virus type 1 isolate=96AM751.3; gene=env 89 atgagagtga aggggataat gaggaattgg caacaatggt ggatatgggg catcttaggc 60 ttttggatgc tattgatgtg taatgcaatg gggaaattgt gggtcacagt ctactatggg 120 gtacctgtgt ggaaagaagc aaaaactact ttattttgtg catcagatgc taaagcatat 180 gagacagaag tgcataatgt ttgggctaca catgcctgtg tacccacaga ccccaaccca 240 caagaaatgg ttttggaaaa tgtaacagaa aagtttaaca tgtgggaaaa taacatggtg 300 gatcagatgc atgaggatat aatcagttta tgggaccaaa gcctaaagcc atgtgtaaag 360 ttgaccccac tctgtgtcac tttaaactgt actgctaata taaccaacaa tgctaatata 420 accaacaatg ctaatataac caactataat aatgaaactg acatgagaaa ttgctctttc 480 aatataacca cagaattaag agataagagg aggcaagtag atgcactctt ttataaactt 540 gatatagtac caattaatga gaattccagt gaatatagat taataaattg taatacctcg 600 gccataacac aagcatgtcc aaaggttact tttgacccaa tccctataca ttattgtgct 660 ccagctggtt atgcgattct aaagtgtaac aataagacat tcaatggaac aggaccatgc 720 aataatgtca gcacagtaca atgtacacat ggaattaagc cagtagtatc aactcaatta 780 ctgttaaatg gtagtctagc agaagaagag ataataatta gatctaaaaa tatgacagac 840 aatgccaaaa taataatagt acatcttaat gaatctgtag aaattgtgtg tacaagaccc 900 aacaataata caaggaaaag tgtgaggata ggaccaggac aaacattcta tgcaacagga 960 gaaataatag gaaatataag acaagcatat tgtaacatca gtgaaggcaa atggaataac 1020 actctacaaa gggtaggtga aaaattaaga aaatacttcc ctaataaaac aataagcttt 1080 gcaccatcct caggagggga cctagaaatt acaacacata gctttaattg tagaggagaa 1140 tttttctatt gcaatacatc aaaactgttt aatggtacgt ttaatggtac aaacacttct 1200 aatgatagaa gtaattcgac cattacgctt caatgcagaa taaaacaaat tacaaacatg 1260 tggcaggggg taggacaagc aatgtatgct cctccaatta aaggaaacat aacatgtaaa 1320 tcaaatatca caggactact attaacacgt gatggaggga caaatgacac agagacacca 1380 gagacattca gacctggagg aggagacatg aaggacaatt ggagaagtga attatataaa 1440 tataaagtgg tagaaattaa gccattagga gtagcaccca ctaaggcacg aaggagagtg 1500 gtggagagag aaaaaagagc agtaggaata ggagctgtgt tccttgggtt cttgggagca 1560 gcaggaagca ctatgggcgc agcatcaata acgctgacgg tacaggtcag acaattattg 1620 tctggtatag tgcaacagca aagcaatttg ctgagggcta tagaggcgca acagcacatg 1680 ttgcaactca cagtctgggg cattaagcag ctccaggcaa gagtcttggc tatagaaaga 1740 tacctaaagg atcaacagct cctagggatt tggggctgct ctggaaaact catctgcacc 1800 actgctgtgc cttggaactc tagttggagc aacaaatctg aacgggagat ttgggataac 1860 atgacctgga tgcagtggga tagagaaatt aataattaca cagaaacaat atataggttg 1920 cttgaagtct cgcaaaacca gcaggaaaat aatgaaaggg atttactagc attggacagt 1980 tgaaaaaatc tgtggaattg gtttaatata acaaattggc tgtggtatat aaaaatattc 2040 ataatgataa taggaggctt gataggttta agaataattt ttgctgtgct ctctatagta 2100 aatagagtta ggcaggggta ctcacctttg tcgttgcaga cccttatccc aaccccgagg 2160 gaaccagaca ggctcggaag aatcgaagaa gaaggtggag agcaagacag agacagatca 2220 attcgattag tgaacggatt cttagcactt gtctgggacg acctccggag cctgtgcctt 2280 ttcagctacc accgcttgag agacttcata ttgattgcag cgaggggact acagaggggg 2340 tgggaaactc ttaagtatct ggggagtctt gtacagtatt ggggtctaga gctaaaaaag 2400 agtgctatta gtttgcttga tactatagca atagcagtag ctgaaggaac agatagaatt 2460 atagaattaa cacaaagaat ttgtagagct atccgcaacg tacctagaag aataagacag 2520 ggctttgaag cagctttgca ataa 2544 90 624 DNA Human immunodeficiency virus type 1 isolate=96AM751.3; gene=nef 90 atgggaggca agtggtcaaa acgcagtata gttggatggc ctaaagtaag agaaagaata 60 gcaagaactg atccagcagc agagggagta ggagcagcgt ctcaagactt agataaatat 120 ggggcactta caagcagtaa cacaagtacc aataatgctg attgtgcctg gctggaagcg 180 caagaggagg agggagaagt aggctttcca gtcagacctc aggtaccttt aagaccaatg 240 acttataagt cagcatttga tctcagcttc tttttaaaag aaaagggggg actggatggg 300 ttaatttact gtaagaaaag acaagaaatc ctcgatttgt gggtctatca cacacaaggc 360 tacttccctg attggcaaaa ctatacaccg ggaccaggga tcagatatcc actgaccttt 420 ggatggtgct acaagctagt gccagttgac ccaagggaag tagaagaagc caacgaagga 480 gaggacaact gtttgctaca ccctataagc cagcatggaa tagaagatga agacagagaa 540 gtattaaggt ggaagtttga cagttcccta gcacgcagac acatggcccg cgagctacat 600 ccggagtatt acaaagactg ctga 624 91 1491 DNA Human immunodeficiency virus type 1 isolate=94CY017.41; gene=gag 91 atgggtgcga gagcgtcaat attaagcggg ggaaaattag atgcttggga gaaaattcgg 60 ttaaggccag ggggaaagaa aaaatataga ctgaaacatt tggtatgggc aagcagggag 120 ctggagaaat tctcaattaa ccctggcctt ttagaaacac cagagggatg tagacaaata 180 ataaggcagt tacaaccagc tctccaaaca ggaacagaag aacttaaatc attatataat 240 acagtagtag tcctctactg ggtacatcaa agggtagatg taaaagacac caaggaagct 300 ctagataaaa tagaggaaga acaaaacaag cagaaaacac agcatgcagc agctgacaca 360 gggaacagca gcagtcaaaa ttatcccata gtgcaaaatg cacaagggca aatggtacac 420 caggctatat cacctaggac gttgaatgcc tgggtcaaag tagtagaaga aaaggctttc 480 agcccagaag taatacctat gtttacagca ttatcagaag gagccacccc acaagactta 540 aatactatgc taaacacagt ggggggacat caagcagcta tgcaaatgtt aaaagatacc 600 atcaatgagg aagctgcaga atgggacagg gtacatccag tacatgcagg gcctattcca 660 ccaggccaga tgagagaacc aaggggaagt gacatagcag gaactactag tacccttcag 720 gaacaaatag gttggatgac cagcgatcca cccatcccag tgggagaaat ttataaaaga 780 tggataatcc tgggattaaa taaaatagta agaatgtata gccctgtcag cattttggac 840 ataagacaag ggccaaaaga accctttaga gattatgtgg ataggttctt taaaactcta 900 agagctgagc aagccacaca ggaggtaaaa aactggatga cggacacctt gctggtccaa 960 aatgcgaacc cagattgtag atccatcttg agagcattag gaccaggggc ctcattagaa 1020 gaaatgatga cagcatgtca gggagtggga ggacccagcc ataaagcaag ggttttggct 1080 gaagcaatga gccatgtaca aagtacaaat acaaacataa tgatgcagag aggcaatttt 1140 aggggtcaaa aaagaattaa gtgtttcaac tgtggcaagg aaggacacct agccagaaat 1200 tgcagggccc ctaggaaaaa gggctgctgg aaatgtggaa aggaaggaca tcaaatgaaa 1260 gattgcactg agagacaggc taatttttta gggaaaattt ggccttccaa caaagggagg 1320 ccaggaaatt ttcctcagag cagaacagag ccaacagccc caccagcaga gaacttgaga 1380 atgggggaag agataacctc ctccctgaag caggaactgg agaccaggga accatacaat 1440 cctgcaattt ccctcaaatc actctttggc aacgacccct tgttacagta a 1491 92 3012 DNA Human immunodeficiency virus type 1 isolate=94CY017.41; gene=pol 92 ttttttaggg aaaatttggc cttccaacaa agggaggcca ggaaattttc ctcagagcag 60 aacagagcca acagccccac cagcagagaa cttgagaatg ggggaagaga taacctcctc 120 cctgaagcag gaactggaga ccagggaacc atacaatcct gcaatttccc tcaaatcact 180 ctttggcaac gaccccttgt tacagtaaag atagagggac agctaaaaga agctctatta 240 gatacaggag cagatgatac agtgttagaa gaaataaatt tgccaggaaa atggaaacca 300 aaaatgatag ggggaattgg aggttttatc aaagtaagac aatatgatca gatagctata 360 gaaatttgtg gaaaaagggc cataggtaca gtattagtag gacctacccc tgtcaacata 420 atcggaagaa atatgttggt tcagcttggt tgtactttaa attttccaat tagtcctatt 480 gaaactgtac cagtaaaatt aaagccagga atggatggtc caaaggttaa acaatggcca 540 ttgacagaag aaaaaataaa agcattaaca gaaatctgta aagaaatgga aaaggaagga 600 aaaatttcaa aaattgggcc tgaaaatcca tacaacactc cagtgtttgc tataaagaaa 660 aaagacagca ctaaatggag aaaattagta gattttagag aactcaataa gagaactcaa 720 gacttctggg aagttcagtt aggaatacca catccagcag gattaaaaaa gaaaaaagca 780 gtaacagtac ttgatgtggg ggacgcatat ttttccgttc ccttacatga agacttcaga 840 aaatatactg cattcaccat acctagtacc aacaatgaga caccaggagt taggtatcag 900 tacaatgtac ttccacaggg atggaaagga tcaccagcaa tattccagag tagcatgaca 960 aagatcttag agccctttag atcaaagaat acagaattaa tcatctacca atacatggat 1020 gacttgtatg taggatctga tttagaaata agccagcata gagtaaaaat agaggaatta 1080 agggctcact tattgaaatg gggattttat acaccagaca aaaaacatca gaaagaacct 1140 ccatttcttt ggatgggata tgagcttcat cctgacaaat ggacagtcca gcctataaag 1200 ctgccagaaa aagacagctg gactgtcaat gatatacaga aattagtagg gaaattaaat 1260 tgggcaagtc agatttatgc agggattaaa gtaaagcaac tgtgtaaact ccttagagga 1320 gccaaagcac taacagacat agtaacactg actaaagaag cagagttaga attagaagag 1380 aacagggaaa ttttaaaaac ccctgtacat ggggtatact atgacccatc aaaagactta 1440 atagcagaaa tacagaaaca agggcaagac caatggacat atcaaattta tcaggaaccc 1500 tttaagaatc tgaaaacagg gaaatatgca aaaaggaggt ccacccacac taatgatata 1560 aaacagttaa cagaagcagt acaaaaaata accatggaaa gcatagtgat atggggaaag 1620 actcctaaat ttaaattacc catacaaaag gaaacatggg agacatggtg ggcggagtat 1680 tggcaggcta cctggattcc tgagtgggag tttgtcaata cccctcctct agtaaaactg 1740 tggtaccagt tagaaaaaga acccatagca ggagcagaaa ctttctatgt agatggggca 1800 gctaatagag agactaaact aggaaaggca gggtatgtca ctgacagagg aagacaaaaa 1860 attgtctccc tgacggagac aacaaatcaa aagactgaat tacatgcaat ctatttggct 1920 ttacaggatt caggattaga agtgaacata gtgacagatt cacagtatgc attaggaatc 1980 attcaagcac aaccagaaag gagtgaatca gagatagtca atcaaataat agaaaaatta 2040 atagaaaagg aaagggtcta cctatcatgg gtaccagcac acaaagggat tggaggaaat 2100 gaacaagtag acaaattagt cagttctgga atcaggaaag tgctattttt agatgggata 2160 gataaggctc aagaggaaca tgaaagatat cacagcaatt ggagagcaat ggctcatgac 2220 tttaatctac cacctgtagt agcaaaagaa atagtagcta gctgtgataa atgtcagcta 2280 aaaggggaag ccatgcatgg acaagtagac tgtagtccag gaatatggca actagattgc 2340 acacatcttg aaggaaaagt tatcctggtg gcagtccatg tggccagtgg ctatatagaa 2400 gcagaagtca tcccaacaga aacaggacag gatacagcat actttatatt aaaactagca 2460 ggaagatggc cagtaaaagt aatacataca gacaatgggc ccaatttcat cagtgcaaca 2520 gttaaggcag cctgttggtg ggcaggtatc caacaagaat ttgggattcc ctacaatccc 2580 caaagtcaag gagtagtgga atctatgaat aaagaattaa agaaaatcat agggcaggta 2640 agagatcaag ctgaacacct taagacagca gtacaaatgg cagtattcat tcacaatttt 2700 aaaagaaaag gggggattgg gggatacagt gcaggggaaa gaataataga cataatagca 2760 acagatatac aaactaaaga actacaaaga caaattacaa aaattcaaaa ttttcgggtt 2820 tattacaggg acagcagaga tccaatttgg aaaggaccag caaaactcct ttggaaaggt 2880 gaaggggcag tagtaataca agacaatagt gacataaagg tagtaccaag aagaaaagca 2940 aagatcatta gggattatgg aaaacagatg gcaggtgatg attgtgtggc aggtagacag 3000 gatgaggatt ag 3012 93 579 DNA Human immunodeficiency virus type 1 isolate=94CY017.41; gene=vif 93 atggaaaaca gatggcaggt gatgattgtg tggcaggtag acaggatgag gattagaaca 60 tggaacagtt tagttaaaca tcatatgtat atttcaagga aagctaaagg ttgggtctat 120 aaacatcact atgaaagcag aaatccaaga ataagttcag aagtacacat cccgctaggg 180 gaggctagaa taatagtaag aacatattgg ggtctgcaca taggagaaaa agactggcac 240 ttgggtcatg gagtctccat agaatggagg caaaacaggt atcatacaca aatagaccct 300 gatctggcag accatctaat ccatctgtat tattttgact gtttttcaga atctgccata 360 aggaaagcca taataggaga aatagttagt cctaggtgtg aatatcaagc aggacataac 420 aaggtagggt ctctgcaata tttggcattg aaagcagtag tagcttcaac aaggacaaag 480 ccacctttgc ctagtgttag gaaattagta gaggatagat ggaacaagcc ccagaagacc 540 aagggccaca gagggagcca tacaatgaat ggatgttag 579 94 291 DNA Human immunodeficiency virus type 1 isolate=94CY017.41; gene=vpr 94 atggaacaag ccccagaaga ccaagggcca cagagggagc catacaatga atggatgtta 60 gaactgttag aggagctcaa gcaggaagct gttagacatt tccctaggca ctggctacat 120 ggcctaggac aatacatcta taatacctat ggggatacct gggaaggagt tgaagttatc 180 ataagatatc tgcaacaact actgtttgtc catttcagaa ttgggtgcca acatagcagg 240 ataggcatta ttcgaagaag aagagtaagg gatggagcca gtagacccta a 291 95 2655 DNA Human immunodeficiency virus type 1 isolate=94CY017.41; gene=tat 95 atggagccag tagaccctaa actagagccc tggaaccatc cgggaagtca gcctaaaact 60 gcttgtacca aatgttattg taaacgctgt tgctatcatt gccagttgtg ctttataaac 120 aaaggcttag gcatctccta cggcaggaag aagcgacgac cccgacgaaa gccttctcca 180 agcaataagg accatcaaaa tcctatacca aagcagtaag tagtagtaat taatatatgt 240 aatgttacct ttagtaatat tggcaatagt aggactgata gtagctttaa tcttagcaat 300 agttgtatgg actatagtat tcatagaata taagaaaatt aagaagcaaa ggaaaataga 360 ctggttaatc aaaagaataa gtgagagagc agaagacagt ggcaatgaga gtgatgggga 420 cacagaggaa ctatcagcac ttgtggagag ggggcatctt gattttgggg atgttaataa 480 tgtgtaaagc tacagatttg tgggtcacag tatactatgg agtacctgtg tggaaagatg 540 cagataccat cctattttgt gcatcagatg ctaaagcata tgatacagaa gtgcataatg 600 tatgggccac acatgcctgt gtacccacag accccaaccc acaagaaata aacctggaaa 660 atgtaacaga aaattttaat atgtggaaaa ataacatggt agagcagatg caagaagata 720 taatcagctt atgggatcaa agcctaaagc catgtgtaaa attaaccccg ctctgcgtca 780 ttttaaattg tagcaatgcc aataccagca cccatagcaa tagcagtagc acccagagcc 840 ccattaatga agaaataaaa aactgctctt acaatactac cacaatacta agagataaga 900 cacaaaaagt ttattcactg ttttatagac ttgatgtagt acaacttgat gaaagtgaaa 960 ataagaatac atcaggtagt aatactctgt atagactaat aaattgtaat acctcaacca 1020 tcacacaagc gtgtccaaag gtaacctttg agccaattcc tatacattat tgtgccccag 1080 ctggttttgc gattctaaag tgtaaggatc cgagattcaa tggaacaggg tcatgcaaga 1140 atgttagctc agtacaatgt acacatggaa ttaaaccagt agcatcaact caactgctgt 1200 tgaatggcag tctagcagaa ggagggaaaa taatgattag atctgaaaat attacaaaca 1260 atgccaaaaa cataatagtt cagtttacta agcctgtact aattacttgt atcagaccca 1320 acaacaatac aagaaaaagt atacgctttg gaccaggaca agccttctat acaaatgaaa 1380 taatagggga cataagacaa gcacattgta atatcaacaa aacattatgg aatgacactt 1440 tacaaaaggt agctgaacaa ttaagagaga aattccctaa gaaaaccata atctttacta 1500 actcctcagg aggggaccca gaaattacaa cacttagttt taattgtgca ggagaatttt 1560 tctattgcaa tacaacaggc ctgtttaatg gtacgtggtg gaacaatggt acgtggaacg 1620 ggccctacac acctaataac accaatggaa gtataatcct cccatgcaga ataaaacaaa 1680 ttataaacat gtggcagaga gtaggaagag caatgtatgc ccctcccatt gcaggaataa 1740 taaagtgtac atcaaacatt acaggaataa tattgacaag agatggtggt aacaatggga 1800 ctaatgagac cttcagacct ggaggaggag atatgaggga caattggaga agtgaattat 1860 ataaatataa agtagtaaaa cttgaaccac taggagtagc acctaccagg gcaaaaagaa 1920 gagtggtgga gagagaaaaa agagcagttg gactgggagc tgtcttcctt gggttcttgg 1980 gagcagcagg aagcactatg ggcgcggcgt cactaacgct gacggtacag gccagacaat 2040 tattgtctgg tatagtgcaa cagcaaagca atttgctgca ggctatagaa gctcaacagc 2100 atctgttgaa actcacagtc tggggcatta aacagctcca ggcgagggtc ctggctgtgg 2160 aaagatacct aaaggatcaa cagctcctgg gaatttgggg ctgctctgga aaactcatct 2220 gcgccactac tgtgccctgg aacactagtt ggagtaataa gtctcaggat gagatttggg 2280 acaacatgac ctggttgcaa tgggataaag aaattagcaa ttacacaaac ataatatata 2340 ggttacttga agaatcgcaa aaccagcagg aaaagaatga gcaagactta ttggcattag 2400 acaaatgggc agatttgtgg agttggttca acatttcaca ctggctgtgg tatataagaa 2460 tatttataat gatagtagga ggcttgatag gattaagaat agtttttgct ataattactg 2520 tagtaaatag agttaggcag ggatactcac ctgtgtcatt tcagatccct accccaagcc 2580 cagagggtcc cgacaggccc agaggaaccg aagaaggagg tggagagcaa ggcagagaca 2640 gatcgattcg attag 2655 96 2721 DNA Human immunodeficiency virus type 1 isolate=94CY017.41; gene=rev 96 acggcaggaa gaagcgacga ccccgacgaa agccttctcc aagcaataag gaccatcaaa 60 atcctatacc aaagcagtaa gtagtagtaa ttaatatatg taatgttacc tttagtaata 120 ttggcaatag taggactgat agtagcttta atcttagcaa tagttgtatg gactatagta 180 ttcatagaat ataagaaaat taagaagcaa aggaaaatag actggttaat caaaagaata 240 agtgagagag cagaagacag tggcaatgag agtgatgggg acacagagga actatcagca 300 cttgtggaga gggggcatct tgattttggg gatgttaata atgtgtaaag ctacagattt 360 gtgggtcaca gtatactatg gagtacctgt gtggaaagat gcagatacca tcctattttg 420 tgcatcagat gctaaagcat atgatacaga agtgcataat gtatgggcca cacatgcctg 480 tgtacccaca gaccccaacc cacaagaaat aaacctggaa aatgtaacag aaaattttaa 540 tatgtggaaa aataacatgg tagagcagat gcaagaagat ataatcagct tatgggatca 600 aagcctaaag ccatgtgtaa aattaacccc gctctgcgtc attttaaatt gtagcaatgc 660 caataccagc acccatagca atagcagtag cacccagagc cccattaatg aagaaataaa 720 aaactgctct tacaatacta ccacaatact aagagataag acacaaaaag tttattcact 780 gttttataga cttgatgtag tacaacttga tgaaagtgaa aataagaata catcaggtag 840 taatactctg tatagactaa taaattgtaa tacctcaacc atcacacaag cgtgtccaaa 900 ggtaaccttt gagccaattc ctatacatta ttgtgcccca gctggttttg cgattctaaa 960 gtgtaaggat ccgagattca atggaacagg gtcatgcaag aatgttagct cagtacaatg 1020 tacacatgga attaaaccag tagcatcaac tcaactgctg ttgaatggca gtctagcaga 1080 aggagggaaa ataatgatta gatctgaaaa tattacaaac aatgccaaaa acataatagt 1140 tcagtttact aagcctgtac taattacttg tatcagaccc aacaacaata caagaaaaag 1200 tatacgcttt ggaccaggac aagccttcta tacaaatgaa ataatagggg acataagaca 1260 agcacattgt aatatcaaca aaacattatg gaatgacact ttacaaaagg tagctgaaca 1320 attaagagag aaattcccta agaaaaccat aatctttact aactcctcag gaggggaccc 1380 agaaattaca acacttagtt ttaattgtgc aggagaattt ttctattgca atacaacagg 1440 cctgtttaat ggtacgtggt ggaacaatgg tacgtggaac gggccctaca cacctaataa 1500 caccaatgga agtataatcc tcccatgcag aataaaacaa attataaaca tgtggcagag 1560 agtaggaaga gcaatgtatg cccctcccat tgcaggaata ataaagtgta catcaaacat 1620 tacaggaata atattgacaa gagatggtgg taacaatggg actaatgaga ccttcagacc 1680 tggaggagga gatatgaggg acaattggag aagtgaatta tataaatata aagtagtaaa 1740 acttgaacca ctaggagtag cacctaccag ggcaaaaaga agagtggtgg agagagaaaa 1800 aagagcagtt ggactgggag ctgtcttcct tgggttcttg ggagcagcag gaagcactat 1860 gggcgcggcg tcactaacgc tgacggtaca ggccagacaa ttattgtctg gtatagtgca 1920 acagcaaagc aatttgctgc aggctataga agctcaacag catctgttga aactcacagt 1980 ctggggcatt aaacagctcc aggcgagggt cctggctgtg gaaagatacc taaaggatca 2040 acagctcctg ggaatttggg gctgctctgg aaaactcatc tgcgccacta ctgtgccctg 2100 gaacactagt tggagtaata agtctcagga tgagatttgg gacaacatga cctggttgca 2160 atgggataaa gaaattagca attacacaaa cataatatat aggttacttg aagaatcgca 2220 aaaccagcag gaaaagaatg agcaagactt attggcatta gacaaatggg cagatttgtg 2280 gagttggttc aacatttcac actggctgtg gtatataaga atatttataa tgatagtagg 2340 aggcttgata ggattaagaa tagtttttgc tataattact gtagtaaata gagttaggca 2400 gggatactca cctgtgtcat ttcagatccc taccccaagc ccagagggtc ccgacaggcc 2460 cagaggaacc gaagaaggag gtggagagca aggcagagac agatcgattc gattagtgaa 2520 cgggttcttc gcacttgcct gggacgacct acggagcctg tgcctcttca gttaccaccg 2580 cttgagagat tgcatattga ttgcagcgag gactgtggaa cttctgggac actgcagtct 2640 caagggactg agactggggt gggaaggtct caagaatctg tggaatcttc tgttatactg 2700 gggtcgggaa ctgaagaata g 2721 97 246 DNA Human immunodeficiency virus type 1 isolate=94CY017.41; gene=vpu 97 atgttacctt tagtaatatt ggcaatagta ggactgatag tagctttaat cttagcaata 60 gttgtatgga ctatagtatt catagaatat aagaaaatta agaagcaaag gaaaatagac 120 tggttaatca aaagaataag tgagagagca gaagacagtg gcaatgagag tgatggggac 180 acagaggaac tatcagcact tgtggagagg gggcatcttg attttgggga tgttaataat 240 gtgtaa 246 98 2598 DNA Human immunodeficiency virus type 1 isolate=94CY017.41; gene=env 98 atgagagtga tggggacaca gaggaactat cagcacttgt ggagaggggg catcttgatt 60 ttggggatgt taataatgtg taaagctaca gatttgtggg tcacagtata ctatggagta 120 cctgtgtgga aagatgcaga taccatccta ttttgtgcat cagatgctaa agcatatgat 180 acagaagtgc ataatgtatg ggccacacat gcctgtgtac ccacagaccc caacccacaa 240 gaaataaacc tggaaaatgt aacagaaaat tttaatatgt ggaaaaataa catggtagag 300 cagatgcaag aagatataat cagcttatgg gatcaaagcc taaagccatg tgtaaaatta 360 accccgctct gcgtcatttt aaattgtagc aatgccaata ccagcaccca tagcaatagc 420 agtagcaccc agagccccat taatgaagaa ataaaaaact gctcttacaa tactaccaca 480 atactaagag ataagacaca aaaagtttat tcactgtttt atagacttga tgtagtacaa 540 cttgatgaaa gtgaaaataa gaatacatca ggtagtaata ctctgtatag actaataaat 600 tgtaatacct caaccatcac acaagcgtgt ccaaaggtaa cctttgagcc aattcctata 660 cattattgtg ccccagctgg ttttgcgatt ctaaagtgta aggatccgag attcaatgga 720 acagggtcat gcaagaatgt tagctcagta caatgtacac atggaattaa accagtagca 780 tcaactcaac tgctgttgaa tggcagtcta gcagaaggag ggaaaataat gattagatct 840 gaaaatatta caaacaatgc caaaaacata atagttcagt ttactaagcc tgtactaatt 900 acttgtatca gacccaacaa caatacaaga aaaagtatac gctttggacc aggacaagcc 960 ttctatacaa atgaaataat aggggacata agacaagcac attgtaatat caacaaaaca 1020 ttatggaatg acactttaca aaaggtagct gaacaattaa gagagaaatt ccctaagaaa 1080 accataatct ttactaactc ctcaggaggg gacccagaaa ttacaacact tagttttaat 1140 tgtgcaggag aatttttcta ttgcaataca acaggcctgt ttaatggtac gtggtggaac 1200 aatggtacgt ggaacgggcc ctacacacct aataacacca atggaagtat aatcctccca 1260 tgcagaataa aacaaattat aaacatgtgg cagagagtag gaagagcaat gtatgcccct 1320 cccattgcag gaataataaa gtgtacatca aacattacag gaataatatt gacaagagat 1380 ggtggtaaca atgggactaa tgagaccttc agacctggag gaggagatat gagggacaat 1440 tggagaagtg aattatataa atataaagta gtaaaacttg aaccactagg agtagcacct 1500 accagggcaa aaagaagagt ggtggagaga gaaaaaagag cagttggact gggagctgtc 1560 ttccttgggt tcttgggagc agcaggaagc actatgggcg cggcgtcact aacgctgacg 1620 gtacaggcca gacaattatt gtctggtata gtgcaacagc aaagcaattt gctgcaggct 1680 atagaagctc aacagcatct gttgaaactc acagtctggg gcattaaaca gctccaggcg 1740 agggtcctgg ctgtggaaag atacctaaag gatcaacagc tcctgggaat ttggggctgc 1800 tctggaaaac tcatctgcgc cactactgtg ccctggaaca ctagttggag taataagtct 1860 caggatgaga tttgggacaa catgacctgg ttgcaatggg ataaagaaat tagcaattac 1920 acaaacataa tatataggtt acttgaagaa tcgcaaaacc agcaggaaaa gaatgagcaa 1980 gacttattgg cattagacaa atgggcagat ttgtggagtt ggttcaacat ttcacactgg 2040 ctgtggtata taagaatatt tataatgata gtaggaggct tgataggatt aagaatagtt 2100 tttgctataa ttactgtagt aaatagagtt aggcagggat actcacctgt gtcatttcag 2160 atccctaccc caagcccaga gggtcccgac aggcccagag gaaccgaaga aggaggtgga 2220 gagcaaggca gagacagatc gattcgatta gtgaacgggt tcttcgcact tgcctgggac 2280 gacctacgga gcctgtgcct cttcagttac caccgcttga gagattgcat attgattgca 2340 gcgaggactg tggaacttct gggacactgc agtctcaagg gactgagact ggggtgggaa 2400 ggtctcaaga atctgtggaa tcttctgtta tactggggtc gggaactgaa gaatagtgct 2460 attagcttat ttgatactat agcagtagca gtagctgagt ggacagatag ggttatagaa 2520 atagggcaaa gagctttcag agctattctc aacataccta gaagaatcag acagggctta 2580 gaaagggctt tactataa 2598 99 654 DNA Human immunodeficiency virus type 1 isolate=94CY017.41; gene=nef 99 atggggggca agtggtcaaa aaggagcata ccaggatggc ctgctattag ggagagaatg 60 agaagaactc ctccaacagc acaaagaaca gaagcagtgt ctccagcagc accaggagta 120 ggagcagtgt ctcaagattt agctactcat ggagcagtca caagcagtaa tacagcagct 180 actaatcctg attgcgcctg ggtggaagcg caagaagagg agagtgaagt aggcttccca 240 gtcaggccac aggtaccttt aaggccaatg accttcaagg gagcgtttga tctcagcttc 300 tttttaaaag aaaagggggg actggatggg ttaatttact cccagaaaag acaagacatc 360 cttgatatgt gggtctacca cacacaaggc tacttccctg attggcagaa ttacacacca 420 gggccaggga tcagataccc attaacattt ggatggtgct tcaagctagt accagtagag 480 ccatctgagg tagaagaagc tactcaggga gagaacaaca gcttattaca ccctatatgc 540 caacatggag tagatgaccc tgaaagagaa gtgttaagat gggagtttga tagaagcctg 600 gcacggagac acagagcccg agagctgcat ccggagtact acaaagactg ctga 654 100 1476 DNA Human immunodeficiency virus type 1 isolate=94IN476.104; gene=gag 100 atgggtgcga gagcgtcaat attaagaggg ggaaaattag atagatggga aaaaattcgg 60 ttaaggccag ggggaaagaa acattatatg ataaaacact tagtatgggc aagcagggag 120 ctggaaagat ttgcgcttaa ccctggcctt ttagagacgt cagacggatg taaacaaata 180 ataaaacagc tacatccagc tcttaagaca ggaacagagg aacttaggtc attattcaac 240 acagtagcaa ctctctattg tgtacatgca gggatagagg tacgagacac caaggaagcc 300 ttagacaaga tagaggaaga acaaaacaaa agtcagcaaa aaatacagca ggcaaaagag 360 gctgacggaa aggtcagtca aaattatcct atagtgcaaa atctccaagg gcaaatggta 420 caccagcccc tatcacctag aactttgaat gcgtgggtaa aagtaataga ggagaaggct 480 tttagcccag aggtaatacc catgttcaca gcattatcag aaggagccac cccctctgat 540 ttaaacacca tgttaaatac agtgggggga catcaagcag ccatgcaaat gttaaaagat 600 accatcaacg aggaggctgc ggaatgggat agattacatc cagtacatgc agggcctaat 660 ccaccaggcc agatgagaga accaagggga agtgatatag caggaactac tagtaccctt 720 caggaacaaa tagcatggat gacaggtaac ccacctattc cagtgggaga catctataaa 780 agatggataa ttctggggtt aaataaaata gtaagaatgt atagccctgt cagcattttg 840 gacataagac aagggccaaa ggaacccttt agagactatg tagaccggtt ctttaaaact 900 ttaagagctg aacaagctac acaagaagta aaaggttgga tgacagacac cttgttggtc 960 caaaatgcaa acccagattg taagaccatt ttaagagcat taggaccagg ggcttcatta 1020 gaagaaatgg tgacagcatg tcaaggagtg ggaggaccta gccacaaagc aagagtgttg 1080 gctgaggcaa tgagccaatc acatagtaac ataatgatgc agagaggcaa ttttaaaggc 1140 cctaaaagaa ttgttaaatg cttcaactgt ggcaaggaag ggcacatagc cagaaattgc 1200 agggccccta gaaaaagagg ctgttggaaa tgtgggcaag aaggacacca aatgaaagac 1260 tgtactgaga ggcaggctaa ttttttaggg aaaatttggc cttcccacaa ggggaggcca 1320 gggaatttcc ttcaaaacag gccagagcca acagccccac cagcagagag cttcaggttc 1380 aaggagacaa cccccgctcc gaagcaggag tcgaaagaca gggaaccctt aacttccctc 1440 aaatcactct ttggcagcga ccccttgtct caataa 1476 101 3011 DNA Human immunodeficiency virus type 1 isolate=94IN476.104; gene=pol 101 ttttttaggg aaaatttggc cttcccacaa ggggaggcca gggaatttcc ttcaaaacag 60 gccagagcca acagccccac cagcagagag cttcaggttc aaggagacaa cccccgctcc 120 gaagcaggag tcgaaagaca gggaaccctt aacttccctc aaatcactct ttggcagcga 180 ccccttgtct caataaaagt agggggccag ataaaggaag ctctcttaga cacaggagca 240 gatgatacag tattagaaga aatagctttg ccaggaagat ggaaaccaaa aatgatagga 300 ggaattggag gttttatcaa agtaagacag tatgatcaaa tacttataga aatttgtgga 360 aaaaaggcta taggtacagt attagtagga cctacacctg tcaacataat tggaagagat 420 atgttgactc agcttggatg cactctaaat tttccaatta gccccattga aactgtacca 480 gtaaaattaa agccaggaat ggatggccca aaggttaaac agtggccatt gacagaagag 540 aaaataaaag cattaacaga aatttgtaaa gaaatggaga aggaaggaaa aattacaaaa 600 attgggcctg aaaatccata taacactcca gtatttgcca taaaaaggaa ggacagtact 660 aagtggagaa aattagtaga tttcagggag ctcaataaaa gaactcaaga cttttgggaa 720 gttcaattag gaataccaca cccagcaggt ttaaaaaaga aaaaatcagt gacagtactg 780 gatgtggggg atgcatattt ttcagttcct ttagatgaag gcttcgggaa atatactgca 840 ttcaccatac ctagtataaa caatgaaaca ccagggatta gatatcaata taatgtgctt 900 ccacagggat ggaaaggatc accagcaata ttccagagta gcatgacaaa aatcttagag 960 ccctttaggg cacgaaatcc aaaaatagtc atctatcaat atatggatga cttgtatgta 1020 gggtctgact tagaaatagg gcatcataga gcaaaaatag aggagttaag agcacatcta 1080 ttaaagtggg gattcaccac accagataag aaacatcaga aagaaccccc atttctttgg 1140 atggggtatg aactccatcc tgacaaatgg acagtacagc ctataaagct gccagaaaag 1200 gatagctgga ctgtcaatga tatacagaag ttagtgggaa aattaaactg ggcaagtcag 1260 atttacccag ggattaaagt gaggcaactt tgtaaactcc ttaggggggc caaagcacta 1320 acagacatag taccactaac tgaagaagca gaattagaat tagcagagaa cagggaaatt 1380 ctaaaagagc cagtacatgg agtatattat gacccatcaa aagacttaat agctgaaata 1440 cagaaacagg ggcatgacca atggacatat caaatttacc aagaaccatt caaaaatctg 1500 aaaacaggga agtatgcaaa aatgaggact gctcacacta atgatgtaaa acagttaaca 1560 gaggcagtgc aaaaaatagc catagaaagc atagtaatat gggaaagacc cctaaattta 1620 gactacccat ccaaaaagaa acgtgggaga catggtggac agactattgg caggccacct 1680 ggattcctga ttgggagttt gttaataccc ctcccctagt aaaattatgg taccagctag 1740 aaaaagaacc catagtagga gcagaaactt tctatgtaga tggagcagct aatagggaaa 1800 ctaaagtagg aaaagcaggg tatgttactg acagaggaag gcagaaaatt gtttctttaa 1860 ctgaaacaac aaatcagaag actgaattgc aagcaattca gctagctttg caagattcag 1920 gaacagaagt aaacatagta acagactcac agtatgcatt aggaatcatt caagcacaac 1980 cagataaaag tgaatcagag ttagtcaacc aaataataga acaattaata aacaaagaaa 2040 gagtctatct gtcatgggta ccagcacata aaggaattgg agggaatgaa caagtagata 2100 gattagtaag tagtggaatt aggaaagtac tgtttctaga tgggatagat aaggctcaag 2160 aagatcatga aaagtatcac agcaattgga gagcaatggc taatgagttt aatctgccac 2220 ccatagtagc aaaagaaata gtagctagct gtgataaatg ccagctaaaa ggggaagcca 2280 tgcatggaca agtagaccgt agcccaggga tatggcaatt agattgtaca catctagaag 2340 gaaaaatcat cctggtagca gtccatgtag ccagtggcta catagaagca gaggttatcc 2400 cagcagaaac aggacaagaa acagcatact atatactaaa attagcagga agatggccag 2460 tcaaagtaat acatacagac aatggtagta atttcaccag tgctgcagtt aaggcagcct 2520 gttggtgggc aggtatccaa caggaatttg gaattcccta caatccccaa agccagggag 2580 tagtagaatc catgaataaa gaattaaaga aaattatagg gcaggtaaga gaacaagctg 2640 agcaccttaa gacagcagta caaatggcag tattcattca caattttaaa agaaaagggg 2700 ggattggggg gtacagtgca ggggaaagaa caatagacat aatagcaaca gacatacaaa 2760 ctaaagaatt acaaaaccaa attacaaaaa ttcaaaattt tcgggtttat tacagagaca 2820 gcagagaccc catttggaaa ggaccagcca aactgctctg gaaaggtgaa ggggcagtag 2880 taatacaaga taatagtgac ataaaggtag tgccaaggag gaaagcaaaa attattaggg 2940 attatggaaa acagatggca ggtgctgatt gtgtggcagg tagacaggat gaggatcaga 3000 acatggaata g 3011 102 579 DNA Human immunodeficiency virus type 1 isolate=94IN476.104; gene=vif 102 atggaaaaca gatggcaggt gctgattgtg tggcaggtag acaggatgag gatcagaaca 60 tggaatagtt tagtaaaaca ccatatgtat gtttcaagaa gagctagtgg atggttttac 120 agacatcatt atgaaagcag acatccaaaa gtaagtgcag aagtacacat cccattagga 180 gatgctagat tagtaataaa aacatattgg ggtttacaaa caggagaaag agattggcat 240 ttgggtcatg gcgtctccat agaatggaga ttgggaagat atagcacaca agtagaacct 300 ggcctggcag accagctaat ccatatgcat tattttgatt gttttgcaga ctctgccata 360 agaaaagcca tattaggaca catagttatt tctaggtgtg attatcaagc aggacataat 420 aaggtaggat ctctacaata cttggcactg acagcattga taaaaccaaa aaagagaaag 480 ccacctctgc ctagtgttaa gaaattagta gaggatagat ggaacaatcc ccagaagacc 540 agggaccaca gagggaacca tacaatgaat ggacactag 579 103 291 DNA Human immunodeficiency virus type 1 isolate=94IN476.104; gene=vpr 103 atggaacaat ccccagaaga ccagggacca cagagggaac catacaatga atggacacta 60 gagcttctag aggaactcaa gcaggaagct gtcagacact ttcctagacc ttagcttcat 120 agcttaggac aatatatcta tgaaacatat ggggatgctt ggacaggagt cgaagcttta 180 ataagaacac tgcaacaatt actgtttatt catttcagaa ttgggtgcca gcatagcaga 240 ataggcattt tacaacggag aagagcaaga aatggagcca gtagatccta a 291 104 2633 DNA Human immunodeficiency virus type 1 isolate=94IN476.104; gene=tat 104 atggagccag tagatcctaa cctagagccc tggaaccatc caggaagtca gcctaaaact 60 gcttgtaata catgctattg taaacactgt agctaccatt gtctagtttg ctttcagaca 120 aaaggcttag gcatttccta tggcaggaag aagcggagac agcgacgcag cgctcctcca 180 agcagtgagg atcatcaaaa tcttatatca aagcagtaag tatatgtaat ggtgaattta 240 ttagaaagag tagattatag attaggagta ggagcattaa tagtagcatt aatcttagca 300 ataattgtgt ggaccatagc atatctagaa tataggaaat tgttaagaca aagaaaaata 360 aacaggttaa ttgaaagaat tagggaaaga gtagaagaca gtggcaatga gagtgagggg 420 gatactgagg aattgtcaac actggtggat atggggaatc ttaggctttt ggatgctaat 480 gatttataat gtagtaggga acttgtgggt cacagtctat tatggggtac ctgtgtggaa 540 agaagcaaaa actactttat tctgtgcatc agatgctaaa gcttatgaga aggaggtgca 600 taatatctgg gctacacatg cctgtgtacc cacagacccc aacccacaag agatggattt 660 agtaaatgta acagaaaatt ttaacatgtg gaaaaatgac atggtggatc agatgcatga 720 ggatgtaatc agtttatggg atcaaagcct aaagccatgt gtaaagttga ccccactctg 780 tgtcacttta aactgtagta aggttaccaa taatgctact tacaataata ctgatgatat 840 aaaaaattgc tcttttaatg caaccacaga aataagagac aagaaacgca aagagtatgc 900 actgttttat agactcgata tagtaccact aaatgagaat aagaacagct ctagtaacta 960 tagtgagtac atattaataa attgtaatac ctcaaccata acacaagcct gtccaaaggt 1020 ctcttttgac ccaattccta tacattattg tgctccagct ggttttgcga ttctaaagtg 1080 taaagatgag acattcaatg ggacaggacc atgcaaggag gtcagtacag tacaatgtac 1140 acatggaatt aagccagtgg tatcaactca actactgtta aatggtagca cagcagaaaa 1200 agagataata actagatctg aaaatataac agacaatgca aaaactataa tagtacatct 1260 taatgaatcc ataaaaattg tatgtacaag acccaacaat aacacaagaa aaagtataag 1320 gatagggcca ggacaagcat tctatgcaac aaacggcata ataggagaca taagacaagc 1380 acattgtaac attagtgaat ctaactggac taaaacttta caagaggtag gaaaaaaatt 1440 agcaaagcac ttccctaata aaacaataag tttcaaccaa tcctcaggag gggacctaga 1500 aattgtaaca catagcttta attgtggagg agaattcttt tattgtaata catcaagact 1560 gtttaacggt acatacaatg gtacagacat gcctacatac aatggtacaa attccagttc 1620 agacatcatc atgcttccat gcagaataag gcaatttata aacatttggc agaaggtagg 1680 acgagcaatg tatgcccctc ccattgaagg aaacataaca tgtgaatcaa atatcacagg 1740 actactatta gtacgtgatg gaggcgacac aaatagtagc acagagatat tcagacctgg 1800 aggaggagat atgagggaca attggagaag tgaattatat aaatataaag tggtagaaat 1860 taagccatta ggaatagcac ctactgaagc aaaaaggaga gtggtggaga gagaaaaaag 1920 agcagtggga ataggagctg tgttccttgg gttcttggga gtagcaggaa gcactatggg 1980 cgcggcgtca atgacgctga cggtacaggc cagacaattg ttgtctggta tagtgcaaca 2040 gcaaagcaat ttgctgaagg ctatagaggc gcaacagcat atgttgcaac tcacagtctg 2100 gggcattaag cagctccaga caagagtctt ggctatagag agatacctaa aggatcaaca 2160 gctcctaggg atttggggct gctctggaaa agtcatctgc cccactgctg tgccttggaa 2220 ctccagctgg agtaataaat caaaagatga tatttggaat aacatgacct ggatgcagtg 2280 ggataaagag attagtaatt acacaaacac aatataccgg ttgcttgaag aatcgcaaat 2340 ccagcaggaa caaaatggaa aagatttatt agcattggac agttggcaaa atctgtggaa 2400 ttggtttagc ataacaaaat ggctgtggta tataaaaata ttcataatta tagtaggagg 2460 cttgataggt ttgagaataa tttttgctgt gctatctata gtaaatagag ttaggcaggg 2520 atactcacct ttgtcgttgc agacccttac cccagacccg agggaacccg acaggctcag 2580 aggaatcgaa gaagaaggtg gagagcaaga caaagacaga tccattcgat tag 2633 105 2651 DNA Human immunodeficiency virus type 1 isolate=94IN476.104; gene=rev 105 atggcaggaa gaagcggaga cagcgacgca gcgctcctcc aagcagtgag gatcatcaaa 60 atcttatatc aaagcagtaa gtatatgtaa tggtgaattt attagaaaga gtagattata 120 gattaggagt aggagcatta atagtagcat taatcttagc aataattgtg tggaccatag 180 catatctaga atataggaaa ttgttaagac aaagaaaaat aaacaggtta attgaaagaa 240 ttagggaaag agtagaagac agtggcaatg agagtgaggg ggatactgag gaattgtcaa 300 cactggtgga tatggggaat cttaggcttt tggatgctaa tgatttataa tgtagtaggg 360 aacttgtggg tcacagtcta ttatggggta cctgtgtgga aagaagcaaa aactacttta 420 ttctgtgcat cagatgctaa agcttatgag aaggaggtgc ataatatctg ggctacacat 480 gcctgtgtac ccacagaccc caacccacaa gagatggatt tagtaaatgt aacagaaaat 540 tttaacatgt ggaaaaatga catggtggat cagatgcatg aggatgtaat cagtttatgg 600 gatcaaagcc taaagccatg tgtaaagttg accccactct gtgtcacttt aaactgtagt 660 aaggttacca ataatgctac ttacaataat actgatgata taaaaaattg ctcttttaat 720 gcaaccacag aaataagaga caagaaacgc aaagagtatg cactgtttta tagactcgat 780 atagtaccac taaatgagaa taagaacagc tctagtaact atagtgagta catattaata 840 aattgtaata cctcaaccat aacacaagcc tgtccaaagg tctcttttga cccaattcct 900 atacattatt gtgctccagc tggttttgcg attctaaagt gtaaagatga gacattcaat 960 gggacaggac catgcaagga ggtcagtaca gtacaatgta cacatggaat taagccagtg 1020 gtatcaactc aactactgtt aaatggtagc acagcagaaa aagagataat aactagatct 1080 gaaaatataa cagacaatgc aaaaactata atagtacatc ttaatgaatc cataaaaatt 1140 gtatgtacaa gacccaacaa taacacaaga aaaagtataa ggatagggcc aggacaagca 1200 ttctatgcaa caaacggcat aataggagac ataagacaag cacattgtaa cattagtgaa 1260 tctaactgga ctaaaacttt acaagaggta ggaaaaaaat tagcaaagca cttccctaat 1320 aaaacaataa gtttcaacca atcctcagga ggggacctag aaattgtaac acatagcttt 1380 aattgtggag gagaattctt ttattgtaat acatcaagac tgtttaacgg tacatacaat 1440 ggtacagaca tgcctacata caatggtaca aattccagtt cagacatcat catgcttcca 1500 tgcagaataa ggcaatttat aaacatttgg cagaaggtag gacgagcaat gtatgcccct 1560 cccattgaag gaaacataac atgtgaatca aatatcacag gactactatt agtacgtgat 1620 ggaggcgaca caaatagtag cacagagata ttcagacctg gaggaggaga tatgagggac 1680 aattggagaa gtgaattata taaatataaa gtggtagaaa ttaagccatt aggaatagca 1740 cctactgaag caaaaaggag agtggtggag agagaaaaaa gagcagtggg aataggagct 1800 gtgttccttg ggttcttggg agtagcagga agcactatgg gcgcggcgtc aatgacgctg 1860 acggtacagg ccagacaatt gttgtctggt atagtgcaac agcaaagcaa tttgctgaag 1920 gctatagagg cgcaacagca tatgttgcaa ctcacagtct ggggcattaa gcagctccag 1980 acaagagtct tggctataga gagataccta aaggatcaac agctcctagg gatttggggc 2040 tgctctggaa aagtcatctg ccccactgct gtgccttgga actccagctg gagtaataaa 2100 tcaaaagatg atatttggaa taacatgacc tggatgcagt gggataaaga gattagtaat 2160 tacacaaaca caatataccg gttgcttgaa gaatcgcaaa tccagcagga acaaaatgga 2220 aaagatttat tagcattgga cagttggcaa aatctgtgga attggtttag cataacaaaa 2280 tggctgtggt atataaaaat attcataatt atagtaggag gcttgatagg tttgagaata 2340 atttttgctg tgctatctat agtaaataga gttaggcagg gatactcacc tttgtcgttg 2400 cagaccctta ccccagaccc gagggaaccc gacaggctca gaggaatcga agaagaaggt 2460 ggagagcaag acaaagacag atccattcga ttagtgaacg gattcttagc acttgcctgg 2520 gacgatctac ggagcctgtg cctcttcagt tgccaccgat tgagagactt catattggtt 2580 gcagcgagag cggtggaact tctgggacgc agcagtctca ggggactaca gagggggtgg 2640 gaagccctta a 2651 106 261 DNA Human immunodeficiency virus type 1 isolate=94IN476.104; gene=vpu 106 atggtgaatt tattagaaag agtagattat agattaggag taggagcatt aatagtagca 60 ttaatcttag caataattgt gtggaccata gcatatctag aatataggaa attgttaaga 120 caaagaaaaa taaacaggtt aattgaaaga attagggaaa gagtagaaga cagtggcaat 180 gagagtgagg gggatactga ggaattgtca acactggtgg atatggggaa tcttaggctt 240 ttggatgcta atgatttata a 261 107 2574 DNA Human immunodeficiency virus type 1 isolate=94IN476.104; gene=env 107 atgagagtga gggggatact gaggaattgt caacactggt ggatatgggg aatcttaggc 60 ttttggatgc taatgattta taatgtagta gggaacttgt gggtcacagt ctattatggg 120 gtacctgtgt ggaaagaagc aaaaactact ttattctgtg catcagatgc taaagcttat 180 gagaaggagg tgcataatat ctgggctaca catgcctgtg tacccacaga ccccaaccca 240 caagagatgg atttagtaaa tgtaacagaa aattttaaca tgtggaaaaa tgacatggtg 300 gatcagatgc atgaggatgt aatcagttta tgggatcaaa gcctaaagcc atgtgtaaag 360 ttgaccccac tctgtgtcac tttaaactgt agtaaggtta ccaataatgc tacttacaat 420 aatactgatg atataaaaaa ttgctctttt aatgcaacca cagaaataag agacaagaaa 480 cgcaaagagt atgcactgtt ttatagactc gatatagtac cactaaatga gaataagaac 540 agctctagta actatagtga gtacatatta ataaattgta atacctcaac cataacacaa 600 gcctgtccaa aggtctcttt tgacccaatt cctatacatt attgtgctcc agctggtttt 660 gcgattctaa agtgtaaaga tgagacattc aatgggacag gaccatgcaa ggaggtcagt 720 acagtacaat gtacacatgg aattaagcca gtggtatcaa ctcaactact gttaaatggt 780 agcacagcag aaaaagagat aataactaga tctgaaaata taacagacaa tgcaaaaact 840 ataatagtac atcttaatga atccataaaa attgtatgta caagacccaa caataacaca 900 agaaaaagta taaggatagg gccaggacaa gcattctatg caacaaacgg cataatagga 960 gacataagac aagcacattg taacattagt gaatctaact ggactaaaac tttacaagag 1020 gtaggaaaaa aattagcaaa gcacttccct aataaaacaa taagtttcaa ccaatcctca 1080 ggaggggacc tagaaattgt aacacatagc tttaattgtg gaggagaatt cttttattgt 1140 aatacatcaa gactgtttaa cggtacatac aatggtacag acatgcctac atacaatggt 1200 acaaattcca gttcagacat catcatgctt ccatgcagaa taaggcaatt tataaacatt 1260 tggcagaagg taggacgagc aatgtatgcc cctcccattg aaggaaacat aacatgtgaa 1320 tcaaatatca caggactact attagtacgt gatggaggcg acacaaatag tagcacagag 1380 atattcagac ctggaggagg agatatgagg gacaattgga gaagtgaatt atataaatat 1440 aaagtggtag aaattaagcc attaggaata gcacctactg aagcaaaaag gagagtggtg 1500 gagagagaaa aaagagcagt gggaatagga gctgtgttcc ttgggttctt gggagtagca 1560 ggaagcacta tgggcgcggc gtcaatgacg ctgacggtac aggccagaca attgttgtct 1620 ggtatagtgc aacagcaaag caatttgctg aaggctatag aggcgcaaca gcatatgttg 1680 caactcacag tctggggcat taagcagctc cagacaagag tcttggctat agagagatac 1740 ctaaaggatc aacagctcct agggatttgg ggctgctctg gaaaagtcat ctgccccact 1800 gctgtgcctt ggaactccag ctggagtaat aaatcaaaag atgatatttg gaataacatg 1860 acctggatgc agtgggataa agagattagt aattacacaa acacaatata ccggttgctt 1920 gaagaatcgc aaatccagca ggaacaaaat ggaaaagatt tattagcatt ggacagttgg 1980 caaaatctgt ggaattggtt tagcataaca aaatggctgt ggtatataaa aatattcata 2040 attatagtag gaggcttgat aggtttgaga ataatttttg ctgtgctatc tatagtaaat 2100 agagttaggc agggatactc acctttgtcg ttgcagaccc ttaccccaga cccgagggaa 2160 cccgacaggc tcagaggaat cgaagaagaa ggtggagagc aagacaaaga cagatccatt 2220 cgattagtga acggattctt agcacttgcc tgggacgatc tacggagcct gtgcctcttc 2280 agttgccacc gattgagaga cttcatattg gttgcagcga gagcggtgga acttctggga 2340 cgcagcagtc tcaggggact acagaggggg tgggaagccc ttaaatatct gggaagtctt 2400 gtgcagtatt ggggtctgga actaaaaaag agtgctatta gtctgcttga taccatagca 2460 ataacaatag ctgagggaac agataggatt atagaattta cacaaagaat ttgcagagct 2520 atccgcaaca tacctagaag aataagacag ggttttgaag cagctttgct ataa 2574 108 624 DNA Human immunodeficiency virus type 1 isolate=94IN476.104; gene=nef 108 atggggagca agatgtcaaa aagcagaata gttggatggc ctgaggtaag agaaagaatg 60 aggagaactg agccagcagc agagggagta ggagcagcat ctcaagactt agctaaacat 120 ggagcactta caaccagcaa cacaccaagc aataatgctg ctggtgcctg gctgcaagcg 180 caagaggagg aagaagaagt aggctttcca gtcagacctc aggtgccttt aagaccaatg 240 acttataaag gagcattcga tctcgccttc tttttaaaag aaaagggggg actggatggg 300 ttaatttact ctaagaaaag gcatgaaatc cttgatttat gggtttataa cacacaaggc 360 tacttccctg attggcaaaa ctacacacca ggaccagggg tcagatatcc actgaccttt 420 ggatggtgct acaagctagt accagttgac ccaagtgtag tagaagaggc caacaaagga 480 gaaaacaact gtttgctaca ccctatgagc caacatggaa tggatgatga agatggagaa 540 gtattaaagt ggcagtttga cagcagccta gcacgcagac acatagcccg cgagctacat 600 ccggagtatt acaaagactg ctga 624 109 17 DNA artificial sequence Upstream primer UP1A spanning tRNA primer binding state 109 agtggcgccc gaacagg 17 110 22 DNA artificial sequence Downstream primer Low2 spanning the R/U5 junction in the 3′ long terminal repeat 110 tgaggcttaa gcagtgggtt tc 22 111 28 DNA artificial sequence Upstream UP1AMlu1 primer containing Mlu1 restriction site 111 tctctacgcg tggcgcccga acagggac 28 112 35 DNA artificial sequence Downstream Low1Mlu1 primer containing Mlu1 restriction site 112 accagacgcg tacaacagac gggcacacac tactt 35 

What is claimed is:
 1. A nucleic acid comprising the nucleotide sequence of the genome of a non-subtype B HIV-1 virus, wherein said nucleotide sequence is selected from sequences having SEQ ID NOS: 1 to 11 or a complementary sequence thereof.
 2. The nucleic acid of claim 1, wherein said nucleic acid comprises a nucleotide sequence of at least 12 contiguous bases of said nucleic acid or a complementary sequence thereof.
 3. The nucleic acid of claim 1, wherein said nucleic acid comprises a nucleotide sequence of a LTR of said nucleic acid or a complementary sequence thereof.
 4. The nucleic acid of claim 1, wherein said nucleic acid encodes a polypeptide selected from the group consisting of Gag, Pol, Vif, Vpr, Env, Tat, Rev, Nef and Vpu, wherein the nucleic acid is from the genome of a non-subtype B HIV-1 virus selected from the group consisting of 92RW009.6, 92NG003.1, 92NG083.2, 93BR020.1, 93BR029.4, 90CF056.1, 94CY032.3, 94CY017.41, 96ZM651.8, 96ZM751.3, and 94IN476.104 or a complementary sequence thereof.
 5. A vector comprising a nucleic acid of claim
 1. 6. A cell comprising a nucleic acid of claim
 1. 7. A cell comprising the vector of claim
 5. 8. A polypeptide encoded by a nucleic acid of claim
 1. 9. The polypeptide of claim 8 comprising a contiguous sequence of at least 13 amino acids.
 10. A method for producing a polypeptide of claim 8, comprising the step of growing a cell under conditions such that the encoded polypeptide is produced, said cell comprising the nucleic acid of the polypeptide of claim
 8. 11. A method for producing a polypeptide of claim 8, comprising the step of growing a cell under conditions such that the encoded polypeptide is produced, said cell comprising a vector having the nucleic acid of the polypeptide of claim
 8. 12. A method of inducing serum antibodies that bind at least one polypeptide of claim 8, comprising the step of administering to a mammal, in a physiologically acceptable carrier, an amount of polypeptide of claim 8 sufficient to elicit production of said antibodies.
 13. A method for detecting the presence of antibodies to a non-subtype B HIV-1 virus in a sample comprising the step of contacting said sample with said polypeptide of claim 8 under conditions that allow the formation of an antibody-antigen complex and detecting the complex.
 14. An antibody to a non-subtype B HIV-1 virus, said antibody binding at least one polypeptide of claim 8, wherein said antibody is made by administering to a mammal an amount of said polypeptide in a physiological carrier sufficient to elicit production of said antibody.
 15. A composition comprising the antibody of claim 14, and a physiologically acceptable carrier.
 16. A method for detecting the presence of a non-subtype B HIV-1 virus in a sample comprising the step of contacting said sample with the antibody of claim 14 under conditions that allow the formation of an antibody-antigen complex and detecting said complex.
 17. A kit for detecting the presence of a non-subtype B HIV-1 virus in a sample comprising the antibody of claim
 14. 18. A method of inducing serum antibodies that bind at least one polypeptide of claim 8, comprising the step of administering to a mammal, in a physiologically acceptable carrier, the nucleic acid which encodes said polypeptide(s) and which produces an immunologically sufficient amount of the encoded polypeptide to elicit said antibodies.
 19. An antibody to a non-subtype B HIV-1 virus, said antibody binding at least one polypeptide of claim 8, wherein said antibody is made by administering to a mammal the nucleic acid encoding said polypeptide(s) in a physiologically acceptable carrier, wherein said nucleic acid produces an immunologically sufficient amount of the encoded polypeptide(s) to elicit said antibody.
 20. A composition comprising the antibody of claim 19, and a physiologically acceptable carrier.
 21. A method for detecting the presence of a non-subtype B HIV-1 virus in a sample comprising the step of contacting said sample with an antibody of claim 19 under conditions that allow the formation of an antibody-antigen complex and detecting said complex.
 22. A kit for detecting the presence of a non-subtype B HIV-1 virus in a sample comprising the antibody of claim
 19. 23. A method for detecting the presence of a non-subtype B HIV-1 virus in a sample comprising the steps of: contacting said sample with a nucleic of claim 1; and detecting said nucleic acid bound to the genomic DNA, mRNA or cDNA of the non-subtype B HIV-1 virus.
 24. A nucleic acid probe comprising a sequence of at least 19 contiguous nucleotides of a nucleic acid of claim
 1. 25. A method of detecting the presence of a non-subtype B HIV-1 virus in a biological sample comprising the steps of: contacting the nucleic acid of the biological sample with the nucleic acid probe of claim 24; and detecting the presence or absence of complexes formed between said nucleic acid of the biological sample and said nucleic acid probe.
 26. A method of detecting the presence of a non-subtype B HIV-1 virus in a biological sample comprising the steps of: contacting said biological sample with at least two nucleic acid probes of claim 26; amplifying the RNA of the biological sample via reverse transcription-polymerase chain reaction to produce amplification products; and detecting the presence or absence of amplification products.
 27. A composition comprising the nucleic acid probe of claim
 24. 28. A method for analyzing a first nucleotide sequence comprising comparing the nucleotide sequence of any one of the nucleotide sequences having SEQ ID NOS: 1 to 11 with said first sequence.
 29. A method for analyzing a first amino acid sequence comprising comparing the amino acid sequence of any one of the amino acid sequences set forth in FIGS. 14-22 with said first sequence. 